Methods for producing modified reverse transcriptases

ABSTRACT

The present disclosure provides methods and systems for amplifying and analyzing nucleic acid samples. The present disclosure provides methods for preparing cDNA and/or DNA molecules and cDNA and/or DNA libraries using modified reverse transcriptases.

SEQUENCE LISTING

A “Sequence Listing XML” is submitted herewith in XML file format and(i) the name of the file is BRP01072-US-Seqs.xml; (ii) the date ofcreation is Jul. 7, 2023; and (iii) the size of the file is 104,496bytes and the material in the XML file is incorporated by reference.

BACKGROUND

A common technique used to study gene expression in living cells is toproduce complementary deoxyribonucleic acid (cDNA) from a ribonucleicacid (RNA) molecule. This technique provides a means to study RNA fromliving cells which avoids the direct analysis of inherently unstableRNA. As a first step in cDNA synthesis, the RNA molecules from anorganism are isolated from an extract of cells or tissues of theorganism. After messenger RNA (mRNA) isolation, using methods such asaffinity chromatography utilizing oligo dT (a short sequence ofdeoxy-thymidine nucleotides), oligonucleotide sequences are annealed tothe isolated mRNA molecules and enzymes with reverse transcriptaseactivity can be utilized to produce cDNA copies of the RNA sequence,utilizing the RNA/DNA primer as a template. Thus, reverse transcriptionof mRNA is a key step in many forms of gene expression analyses.Generally, mRNA is reverse transcribed into cDNA for subsequent analysisby primer extension or polymerase chain reaction.

Reverse transcriptase has both an RNA-directed DNA polymerase activityand a DNA-directed DNA polymerase activity. The reverse transcription ofRNA templates may require a primer sequence which is annealed to an RNAtemplate in order for DNA synthesis to be initiated from the 3′ OH ofthe primer. At room temperature, reverse transcriptase enzymes may allowformation of both perfectly matched as well as mismatched DNA/RNAhybrids. In some instances, a reverse transcriptase enzyme can producelarge amounts of non-specific cDNA products as a result of suchnon-specific priming events. The products of non-specific reversetranscription can interfere with subsequent cDNA analyses, such as cDNAsequencing, real-time polymerase chain reaction (PCR), and alkalineagarose gel electrophoresis, among others. Non-specific cDNA templatesproduced by non-specific reverse transcriptase activity can presentparticular difficulties in applications such as real-time PCR. Inparticular, such non-specific cDNA products can give rise to falsesignals which can complicate the analysis of real-time PCR signals andproducts. Thus, the reduction of non-specific reverse transcriptaseactivity may result in greater specificity of cDNA synthesis. Currently,there are no reliable and easy to use methods for improving thespecificity of reverse transcription. The present disclosure satisfiesthese and other needs.

Several approaches may be used for obtaining transcriptome data fromsingle cells. A pioneer approach used reverse transcriptase and oligo-dTprimers with a T7 phage RNA polymerase promoter sequence attached to the5′ end of the oligo-dT run. The resulting cDNA was transcribed intomultiple copies of RNA which were then converted back to cDNA (Phillips,et al., Methods 10(3):283-288 (1996)). This often truncates the cDNAmolecule, losing 5′ sequences of the original mRNA, especially forrelatively long transcripts, and requires multiple rounds of processingwhen starting with low quantity (LQ) of cells, further exacerbating cDNAtruncation. A recent modification (Hashimshony, et al., Cell Rep.2(3):666-673 (2012)) enables multiplex analyses, but this is still 3′end sequence biased. Other methods are based on PCR amplification ofcDNA (Liu, et al., Methods Enzymol. 303:45-55 (1999), Ozsolak, et al.,Genome Res. 20(4):519-525 (2010), Gonzalez, et al., PLoS ONE.5(12):e14418 (2010), Kanamori, et al., Genome Res. 21(7):1150-1159(2011), Islam, et al., Genome Res. 21(7):1160-1167 (2011), Tang, et al.,Nat. Methods. 6(5):377-382 (2009), Kurimoto, et al., Nucleic Acids Res.34(5):e42 (2006), Qiu S, et al., Front Genet. 3:124 (2012)).

These approaches, however, may yield biased representations of sequencesalong the mRNA, and fail to give complete sequences for mRNAs (e.g.,long mRNAs) because DNA templates (e.g., long DNA templates) arediscriminated against even when a long PCR reaction is used.

SUMMARY

In some aspects, the disclosure provides a method for generating anon-naturally occurring enzyme comprising: a) expressing a heterologoussequence encoding said non-naturally occurring enzyme in a host, whereinsaid non-naturally occurring enzyme comprises: a first domain, such as afinger domain, derived from an R2 retrotransposon; a second domain, suchas a thumb domain, derived from an R2 retrotransposon; a third domain,such as a palm domain, derived from an R2 retrotransposon; and anendonuclease domain derived from an R2 retrotransposon; b) purifyingsaid non-naturally occurring enzyme from said host, thereby generatingsaid non-naturally occurring enzyme. In some instances, saidnon-naturally occurring enzyme further comprises a fusion-tag molecule.In other instances, said fusion tag-molecule stabilizes saidnon-naturally occurring enzyme and said fusion-tag molecule is selectedfrom the group consisting of: Fh8, MBP, NusA, Trx, SUMO, GST, SET, GB1,ZZ, HaloTag, SNUT, Skp, T7PK, EspA, Mocr, Ecotin, CaBP, ArsC, IF2-domainI, an IF2-domain I derived tag, RpoA, SlyD, Tsf, RpoS, PotD, Crr, msyB,yjgD, rpoD, and His6. In other cases, said fusion-tag molecule isselected from the group consisting of: His-tag, His6-tag,Calmodulin-tag, CBP, CYD (covalent yet dissociable NorpD peptide), StrepII, FLAG-tag, HA-tag, Myc-tag, S-tag, SBP-tag, Softag-1, Softag-3,V5-tag, Xpress-tag, Isopeptag, SpyTag, B, HPC (heavy chain of protein C)peptide tags, GST, MBP, biotin, biotin carboxyl carrier protein,glutathione-S-transferase-tag, green fluorescent protein-tag, maltosebinding protein-tag, Nus-tag, Strep-tag, and thioredoxin-tag. In someinstances, at least one of said first domain, said second domain, saidthird domain, or said endonuclease domain, is derived from an arthropod.In some instances at least one of said first domain, said second domain,said third domain, or said endonuclease is derived from a vertebrate, anechinoderm, a flatworm, a hydra, or silkmoth. In some instances, saidnon-naturally occurring enzyme has at least 90% identity to SEQ ID NOs:1-20. In some aspects, said host is selected from bacteria, yeast,algae, cyanobacteria, fungi, a plant cell, E. coli, or any combinationthereof. In some instances, said non-naturally occurring enzymecomprises a mutagenized motif-1 sequence. In some instances, saidmutagenized motif-1 sequence has an improved jumping activity ascompared to a wild-type sequence. In some instances, said non-naturallyoccurring enzyme comprises a mutagenized motif 0 sequence. In someinstances, said mutagenized motif 0 sequence has an improved jumpingactivity as compared to a wild-type sequence. In some instances, saidnon-naturally occurring enzyme comprises a mutagenized thumb sequence.In some instances, said mutagenized second domain sequence has animproved single-stranded priming efficiency or an improved processivity.

In some instances, the disclosure provides a non-naturally occurringenzyme, comprising (i) a first domain, such as a finger domain, from anR2 retrotransposon; (ii) a second domain, such as a thumb domain,derived from an R2 retrotransposon; (iii) a third domain, such as a palmdomain, derived from an R2 retrotransposon; and (iv) an endonucleasedomain derived from an R2 retrotransposon. In some instances, saidnon-naturally occurring enzyme has at least 80% identity to SEQ ID NOs:1-20.

In some instances, the disclosure provides a method for simultaneouslyamplifying a ribonucleic acid (RNA) molecule and a deoxyribonucleic(DNA) molecule, comprising: (a) providing a reaction mixture comprisingsaid RNA, DNA and non-naturally occurring enzymes, each of saidnon-naturally occurring enzymes comprising (i) a first domain, such as afinger domain, derived from a non-retroviral transposon or from an R2retrotransposon; (ii) a second domain, such as a thumb domain, derivedfrom an R2 retrotransposon; (iii) a third domain, such as a palm domain,derived from an R2 retrotransposon; and (iv) an endonuclease domainderived from an R2 retrotransposon; and (b) subjecting said reactionmixture to conditions sufficient to amplify said RNA and DNA, therebyyielding amplified products of said RNA and said DNA. In some instances,said DNA is complementary DNA derived from a subset of RNA in saidreaction mixture.

In some instances, the disclosure provides a method for preparing acomplementary deoxyribonucleic acid (cDNA) molecule comprising: (a)partitioning a cell and a non-naturally occurring reverse transcriptase,which cell comprises ribonucleic acid (RNA) molecules; (b) releasingsaid RNA molecules from said cell in said partition; and (c) in saidpartition, using said non-naturally occurring reverse transcriptase tosynthesize a complementary deoxyribonucleic acid (cDNA) library fromsaid RNA molecule, which non-naturally occurring transcriptasesynthesizes said cDNA library at a processivity of 20 nucleotides orlonger. In some instances, said non-naturally occurring reversetranscriptase has at least 80% identity to SEQ ID NOs: 1-20. In someinstances, said partition further comprises: i) one or more acceptornucleic acid molecules; and ii) a non-naturally occurring reversetranscriptase, wherein said non-naturally occurring reversetranscriptase has at least 80% identity to SEQ ID NOs: 1-20.

In some aspects, said partition is a reaction space or chamber that maybe a droplet, a well, or a tube. In some instances, said droplet may beformed by bringing a first phase in contact with a second phase that isimmiscible with the first phase, such as bringing an aqueous phase incontact with an oil phase.

In some instances, the disclosure provides, a method for processing asample comprising various types of ribonucleic acids (RNAs), comprisingusing said RNA molecules to synthesize complementary deoxyribonucleicacid (cDNA) molecules in presence of ribosomal ribonucleic acid (rRNA)molecules blocked from transcription, such that less than 30% of saidcDNA molecules comprise sequences from said rRNA molecules. In someinstances, rRNA may not have been degraded and may be present duringreverse transcription.

In some instances, the disclosure provides, a method for processing amixture comprising ribonucleic acid (RNA) molecules, comprising: (a) insaid mixture, fragmenting said RNA molecules to yield a plurality of RNAfragments; (b) bringing one or more single stranded nucleic sequences incontact with said plurality of RNA fragments, which one or moresingle-stranded nucleic acids sequences have complementarity with atleast a subset of said RNA fragments, thereby providing one or more RNAfragment complexes comprising said one or more single-stranded nucleicacids sequences hybridized to said at least said subset of said RNAfragments; and (c) using a reverse transcriptase to synthesize at leastone complementary deoxyribonucleic acid (cDNA) molecule from said RNA inpresence of said one or more RNA fragment complexes.

In some instances, the disclosure provides a method for sequencing asingle stranded nucleic acid molecule, comprising: (a) providing areaction mixture comprising said single stranded nucleic acid moleculeand a non-naturally occurring enzyme, wherein said non-naturallyoccurring enzyme comprises: a first domain, such as a finger domain,derived from an R2 retrotransposon; a second domain, such as a thumbdomain, derived from an R2 retrotransposon; a third domain, such as apalm domain, derived from an R2 retrotransposon; and an endonucleasedomain derived from an R2 retrotransposon, (b) subjecting said reactionmixture to conditions sufficient to use said non-naturally occurringenzyme to incorporate individual nucleotides into a growing strandcomplementary to said single stranded nucleic acid molecule, whereinincorporation of said individual nucleotides into said growing strandyields detectable signals; and (c) detecting said detectable signals,thereby sequencing said single stranded nucleic acid molecule. In someaspects, said single stranded nucleic acid molecule is an RNA moleculeor a single stranded DNA molecule. In some aspects, said conditionssufficient to directly sequence said single stranded nucleic acidmolecule comprise optic based single-molecule sequencing conditions. Insome aspects, said conditions sufficient to directly sequence saidsingle stranded nucleic acid molecule comprise microscopy basedsingle-molecule sequencing conditions. In some aspects, said conditionssufficient to directly sequence said single stranded nucleic acidmolecule comprise nanopore based single-molecule sequencing conditions.In some aspects, said conditions sufficient to directly sequence saidsingle stranded nucleic acid molecule comprise field-effect transistorsbased single-molecule sequencing conditions.

In some aspects, the disclosure provides a method comprising: (a)preparing a complementary deoxyribonucleic acid (cDNA) molecule from oneor more ribonucleic acid (RNAs), wherein said one or more ribonucleicacid (RNAs) are derived from an in situ tissue of a subject or from afixed ex vivo tissue of said subject with a non-naturally occurringenzyme, wherein said non-naturally occurring enzyme comprises: a firstdomain, such as a finger domain, derived from an R2 retrotransposon; asecond domain, such as a thumb domain, derived from an R2retrotransposon; a third domain, such as a palm domain, derived from anR2 retrotransposon; and an endonuclease domain derived from an R2retrotransposon; thereby generating a cDNA molecule from said in situtissue of said subject or from said fixed ex vivo tissue of saidsubject; and (b) sequencing the said cDNA molecule generated in (a). Insome aspects, said fixed ex vivo tissue of said subject is fixed informaldehyde or in paraffin.

In some aspects, the disclosure provides a method for preparing acomplementary deoxyribonucleic acid molecule comprising: (a) fragmentinga ribonucleic molecule to yield a plurality of RNA fragments; (b)removing a 3′-phosphate group, a 2′-phosphate group, and cyclic 2′3′phosphate from one or more of said RNA fragments, thereby generating oneor more dephosphorylated fragmented RNAs; (c) adding a poly-A tail tosaid one or more dephosphorylated fragmented RNAs; (d) adding, to saidone or more dephosphorylated fragmented RNAs: a primer adaptercomprising an oligo-T sequence; an acceptor adapter; and a non-naturallyoccurring R2 enzyme having a processivity of 20 nucleotides or longerwherein said non-naturally occurring R2 enzyme reverse transcribes asequence from said one or more dephosphorylated fragmented RNAs in a 3′to 5′ order, wherein said R2 enzyme jumps to a 3′-end of said acceptoradapter upon reaching the 5′ end of said one or more dephosphorylatedfragmented RNAs. In some aspects, said acceptor adapter comprises anucleotide analogue. In some aspects, said nucleotide analogue is at the5′ end of said acceptor adapter, of said primer adapter, or both. Someaspects further comprise removing one or more non-annealedprimer-adapter of (d)(i) prior to adding said non-naturally occurring R2enzyme. In some instances, said one or more non-annealed primer-adapteris removed with an immobilized poly A oligo. In some aspects, saidacceptor adapter comprises a 3′-dideoxy nucleotide at theacceptor-adapter 3′-end.

In some aspects, the disclosure provides a method for preparing acomplementary deoxyribonucleic acid molecule comprising: (a) fragmentinga ribonucleic (RNA) molecule to yield a plurality of fragmented RNAfragments; (b) adding, to said one or more fragmented RNAs: a primeradapter; an acceptor adapter; and a non-naturally occurring R2 enzymehaving a processivity of 20 nucleotides or longer wherein saidnon-naturally occurring R2 enzyme primes the reverse transcription usinga plurality of ssDNA primers that are not complementary to a template,wherein said R2 enzyme jumps to a 3′-end of said acceptor adapter uponreaching the 5′ end of said fragmented RNAs.

In some aspects, the disclosure provides a method for preparing acomplementary deoxyribonucleic acid molecule comprising: a) fragmentinga ribonucleic (RNA) molecule to yield a plurality of fragmented RNAfragments; b) adding, to said one or more fragmented RNAs: i. a primeradapter; ii. an acceptor adapter; and enzyme; wherein said enzyme primesthe reverse transcription using a plurality of ssDNA primers that arenot complementary to a template, wherein said enzyme jumps to a 3′-endof said acceptor adapter upon reaching the 5′ end of said fragmentedRNAs. In some instances, said enzyme is a non-naturally occurring R2enzyme.

In some aspects, the disclosure provides a method for preparing acomplementary deoxyribonucleic acid molecule comprising: a) adding to anon-fragmented ribonucleic (RNA) molecule: i. a primer adapter; ii. anacceptor adapter; and iii. an enzyme wherein said enzyme primes thereverse transcription using a plurality of ssDNA primers that are notcomplementary to a template, wherein said enzyme jumps to a 3′-end ofsaid acceptor adapter upon reaching the 5′ end of said fragmented RNAs.In some instances, said enzyme is a non-naturally occurring R2 enzyme.

In some aspects, the disclosure provides a method for depleting aplurality of ribonucleic acid (RNAs) from a sample, comprising: (a)synthesizing a complementary deoxyribonucleic acid (cDNA) molecule froma ribonucleic acid template from said sample, (b) incorporating a firstadapter molecule to a 3′ of said synthesized cDNA molecule andincorporating a second adapter molecule to a 5′ end of said synthesizedcDNA; (c) performing at most 10 cycles of a polymerase chain reaction(PCR) with a modified-oligo probe complementary to said rDNA sequence,wherein said modified-oligo probe is configured to permit binding ofsaid probe to a solid support, thereby generating a hybridized productthat is bound to said solid support in the reaction mixture; (d)removing the synthesized cDNA from said reaction mixture while thehybridized product is bound to said solid support, thereby depletingsaid plurality of ribonucleic acid (RNAs) from said sample.

In some aspects the disclosure provides a method for depleting aplurality of ribonucleic acid (RNAs) from a sample, comprising: a)synthesizing an asymmetric double stranded deoxyribonucleic acidmolecule that is protected from enzymatic degradation at a first 5′ endand unprotected at a second 5′ end from a ribonucleic (RNA) molecule byadding to a reaction vessel comprising an RNA molecule i. a primer,wherein said primer comprises a modification at its 5′ end that isconfigured to prevent enzymatic degradation by a 5′ to 3′ exonuclease;and ii. an enzyme; under conditions sufficient to allow for thesynthesis of said asymmetric double stranded deoxyribonucleic acidmolecule; (b) adding a 5′ to 3′ exonuclease to the product of step (a),thereby generating a ssDNA having a pre-determined polarity; and (c)depleting said plurality of RNAs from the product of said (b) byhybridizing one of more probes to said plurality of RNAs and performinga pull-down reaction.

In some aspects, the disclosure provides a method for preparing a samplefor ribonucleic acid (RNA) sequencing, comprising: (a) individuallylabeling a plurality of single cells with a plurality of uniquebarcodes; (b) combining said plurality of single cells in a single pot;(c) performing an RNA sequencing reaction on said plurality of singlecells; (d) selecting a cell of interest based on said RNA sequencingreaction and identifying a unique barcode associated with said cell ofinterest, wherein said selecting and said identifying are performed in acomputer program product; (e) hybridizing a primer to said uniquebarcode associated with said cell of interest and performing anamplification reaction in said hybridized sample, thereby generating aplurality of amplicons.

In some aspects, the disclosure provides a method for preparing a samplefor ribonucleic acid (RNA) sequencing, comprising: (a) dissociating atissue sample in a lysis reaction, thereby generating a plurality ofnucleic acid templates from said dissociated sample, wherein saidnucleic acid templates comprise ribonucleic acid; (b) synthesizing acomplementary deoxyribonucleic acid (cDNA) molecule from said pluralityof nucleic acid templates from said dissociated sample, wherein saidcDNA molecule is synthesized with a non-naturally occurring R2 enzymehaving a processivity of 20 nucleotides or longer, wherein the synthesisis performed in the presence of one or more regents used in said lysisreaction or in the presence of a plurality of cell debris from saidtissue sample.

Additional aspects and advantages of the present disclosure will becomereadily apparent to those skilled in this art from the followingdetailed description, wherein only illustrative embodiments of thepresent disclosure are shown and described. As will be realized, thepresent disclosure is capable of other and different embodiments, andits several details are capable of modifications in various obviousrespects, all without departing from the disclosure.

Accordingly, the drawings and description are to be regarded asillustrative in nature, and not as restrictive.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications, and NCBI accessionnumbers mentioned in this specification are herein incorporated byreference to the same extent as if each individual publication, patent,patent application, or NCBI accession number was specifically andindividually indicated to be incorporated by reference. To the extentpublications and patents, patent applications, or NCBI accession numbersincorporated by reference contradict the disclosure contained in thespecification, the specification is intended to supersede and/or takeprecedence over any such contradictory material.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the disclosure are set forth with particularity inthe appended claims. A better understanding of the features andadvantages of the present disclosure will be obtained by reference tothe following detailed description that sets forth illustrativeinstances, in which the principles of the disclosure are utilized, andthe accompanying drawings (also “Figure” and “FIG.” herein), of which:

FIG. 1A illustrates the R2 N-terminal Domain. This figure illustratesthe comparison of the conserved sequence motifs in the amino-terminaldomains of the R2 elements. This figure also highlights the CCHH zincfinger and the KWRK c-myb DNA-binding motifs. The continuation of theN-terminal domain alignment is shown in FIG. 1B.

FIG. 1B illustrates the R2 N-terminal domain. This figure is acontinuation of the alignment from FIG. 1A and as such, also illustratesthe comparison of the conserved sequence in the N-terminal domains of R2elements. The following sequences at the C-terminal are the RT andendonuclease domains, which are not shown in this figure.

FIG. 1C illustrates a schematic diagram of the amino acid sequencesimilarity of nine arthropod R2 elements whereby the N-terminal domainis labeled.

FIG. 2 illustrates the R2 reverse transcriptase. This figure illustratesthe comparison of the conserved sequence motifs of the N-terminalportion of the reverse transcriptase R2 elements. This figure highlightsmotif-1 and motif 0. Both motifs are subjected toengineering/mutagenesis in the method of the present disclosure.

FIG. 3 illustrates the R2 reverse transcriptase (RT) thumb domain. Thisfigure illustrates the comparison of the conversed sequence motifs. TheR2 RT thumb domain is subjected to engineering/mutagenesis in the methodof the present disclosure.

FIG. 4 illustrates the R2 reverse transcriptase (RT) thumb domain. Thisfigure is a continuation of FIG. 3 and illustrates a comparison of theconserved sequence motifs. The R2 RT thumb domain is subjected toengineering/mutagenesis in the method of the present disclosure.

FIG. 5A illustrates a method for rRNA sequence depletion as described inthe present disclosure whereas the rRNA depletion is integrated into theprocess of sample preparation. This figure illustrates the differentsteps of the procedure whereby during or right after RNA samplefragmentation, the ssDNA (DNA-sponge), which is complementary to rRNA,is included in the library preparation reaction. DNA-sponges are largessDNA fragments that are at least partially complementary to a sequenceof an rRNA subunit.

FIG. 5B illustrates a method for rRNA sequence depletion as described inthe present disclosure and illustrated in FIG. 5A. FIG. 5B, however,illustrates a method in which an RCA product, which is rRNAcomplementary, is used instead of the circular ssDNA (DNA-sponge).

FIG. 6 illustrates the ability of in situ RNA-seq to allow genome-wideprofiling of gene expression in situ in fixed cells and tissues. Thisfigure illustrates the steps of in situ RNA-seq whereby RNA is convertedinto cDNA and either directly sequenced using single-molecule method orconverted to a sequencing library. This figure also illustrates thespatial-specific barcoding technique in which a glass plate with printedbarcoded primer oligonucleotide is used.

FIG. 7 illustrates the general Poly A based method of RNA-sequencinglibrary prep. This figure illustrates the different steps starting withRNA fragmentation. The methods for fragmentation include spontaneous RNAmagnesium induced degradation or enzymatic cleavage. This figureillustrates that depending on which method is used, the cleavage mayresult in 3′-OH or cyclic 2′, 3′-phosphate at the 3′-end of the RNAfragment.

FIG. 8 illustrates a shorter version of the Poly A based method of RNAsequence library prep described in FIG. 7 . This figure illustrates amethod whereby engineered T4 PNK is used, thus, allowing thesimultaneous use of both enzyme T4 PNK and Poly A polymerase withoutbreaking the protocol into two steps as in FIG. 7 .

FIG. 9 illustrates the library product and adapter-dimer artifacts thatcan be generated in the reaction with the R2 enzyme. The adapter dimersartifacts including acceptor extension are prevented by 3′-dideoxynucleotide at the acceptor-adapter 3′-end (alternatively differentextension blockers can be applied like 3′phospho-dNTP, 3′amino-dNTP).The artifacts primed by primer-adapter (including poly-T sequence) areremoved from the reaction with oligo-A attached to magnetic beads. Theartifacts are primed without annealing (template primer duplexformation) so the primer sequence remained single-stranded.

FIG. 10 illustrates 3′-end priming and extension with ssDNAprimer-adapter and R2. In this mechanism, extension is primed on the3′-end of the template by ssDNA primer without complementary sequenceannealing to the template. This figure illustrates that the libraryproducts are a full length copy of the template.

FIG. 11 illustrates a method of random priming by random fragmentation.This figure illustrates the first step, whereby the RNA sample isfragmented. This figure also illustrates the second step, whereby theRNA sample is mixed with primer-adapter (ssDNA), R2 enzyme, andacceptor-adaptor (ssDNA or RNA). The figure illustrates the third step,the cleanup by solid phase reversible immobilization (SPRI), wherebysize selection is used to remove some adapter-adapter dimer artifacts.The figure illustrates the last step, which is a polymerase chainreaction (PCR) amplification using primer complementary to both theprimer- and the acceptor-adapter.

FIG. 12 illustrates the same method described in FIG. 11 , however, witha different cleanup reaction. This figure illustrates the fragmentationstep, the 3′-end priming, and finally the cleanup reaction, wherebyadapter dimers and artifacts are removed with oligo-magnetic beadscomplementary to the ssDNA adapter.

FIG. 13 illustrates a phylogenic tree, which highlights the inferredevolutionary relationships between non-LTR retroelements and silkmoth,here with a minimum 27% identity to silkmoth, and R2 retrotransposonfocused on fragments of RT-endonuclease.

FIG. 14 illustrates the silkmoth R2 reference sequence (SEQ ID NO: 97).

FIG. 15 illustrates motif-1 point mutations.

FIG. 16 illustrates motif 0 point mutations.

FIG. 17 illustrates thumb subunit substitutions, continued in FIG. 18 .

FIG. 18 illustrates thumb subunit substitutions. This figure is acontinuation of FIG. 17 .

FIG. 19 illustrates a method to remove specific artifacts.

FIG. 20 illustrates a computer system that is programmed or otherwiseconfigured to implement methods provided herein.

FIG. 21 illustrates the steps of a method for abundant (rRNA) sequencedepletion with PCR extension and biotinylated oligo-primers.

FIG. 22 illustrates the steps of a method for abundant (rRNA) sequencedepletion with 5′-end protected oligos (PCR primer).

FIG. 23 illustrates the steps of a method for sequencing a pool ofsingle cells where each single cell is labeled with a unique barcode asa selective target for PCR amplification.

FIG. 24 illustrates the steps of a method for direct RNA-seq librarypreparation from tissue/cell biomass without RNA purification.

FIG. 25 illustrates bioanalyzer traces in Example 25.

FIG. 26 illustrates library molecule structure in Example 25.

DETAILED DESCRIPTION

While various embodiments of the disclosure have been shown anddescribed herein, it will be obvious to those skilled in the art thatsuch embodiments are provided by way of example only. Numerousvariations, changes, and substitutions may occur to those skilled in theart without departing from the disclosure. It should be understood thatvarious alternatives to the embodiments of the disclosure describedherein may be employed.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which the present disclosure belongs. In case of conflict,the present application including the definitions will control. Also,unless otherwise required by context, singular terms shall includepluralities and plural terms shall include the singular. Allpublications, patents and other references mentioned herein areincorporated by reference in their entireties for all purposes as ifeach individual publication or patent application were specifically andindividually indicated to be incorporated by reference, unless onlyspecific sections of patents or patent publications are indicated to beincorporated by reference. In order to further define the presentdisclosure, the following terms, abbreviations and definitions areprovided.

The term “about” generally refers to variations in the numericalquantity that may occur, for example, through typical measuring andliquid handling procedures used for making concentrates or solutions inthe real world; through inadvertent error in these procedures; throughdifferences in the manufacture, source, or purity of the ingredientsemployed to make the compositions or to carry out the methods; and thelike. The term “about” also encompasses amounts that differ due todifferent equilibrium conditions for a composition resulting from aparticular initial mixture. Whether or not modified by the term “about”,the claims include equivalents to the quantities. In some instances, theterm “about” means within 10% of the reported numerical value, or within5% of the reported numerical value, or within 20% of the reportednumerical value.

The indefinite articles “a” and “an” preceding an element or componentof the present disclosure are intended to be nonrestrictive regardingthe number of instances, i.e., occurrences of the element or component.Therefore “a” or “an” should be read to include one or at least one, andthe singular word form of the element or component also includes theplural unless the number is meant to be singular.

As used herein, “non-LTR retrotransposon” generally refers to naturallyoccurring proteins encoded by non-LTR retrotransposons and polypeptidefragments thereof which possess reverse transcriptase activity, as wellas proteins or polypeptides derived therefrom which contain one or moreamino acid substitutions that either enhance the reverse transcriptaseactivity thereof or have no deleterious effect thereon. A class ofnon-LTR retrotransposon is R2 proteins or polypeptides. Thus, as usedherein, “R2 protein or R2 enzyme or polypeptide or a functional fragmentthereof” refers to naturally occurring proteins encoded by R2 elementsand polypeptide fragments thereof which possess reverse transcriptaseactivity, as well as proteins or polypeptides derived therefrom whichcontain one or more amino acid substitutions that either enhance thereverse transcriptase activity thereof or have no deleterious effectthereon.

As used herein, the terms “variant,” “modified,” “non-naturallyoccurring,” and “mutant” are synonymous and refer to a polypeptide orenzyme differing from a specifically recited polypeptide or enzyme byone or more amino acid insertions, deletions, mutations, andsubstitutions, created using, e.g., recombinant DNA techniques, such asmutagenesis. Guidance in determining which amino acid residues may bereplaced, added, or deleted without abolishing activities of interest,may be found by comparing the sequence of the particular polypeptidewith that of homologous polypeptides, e.g., yeast or bacterial, andminimizing the number of amino acid sequence changes made in regions ofhigh homology (conserved regions) or by replacing amino acids withconsensus sequences. In some instances, the terms “derivative,”“variant,” “modified,” “non-naturally occurring,” and “mutant” are usedinterchangeably.

The terms “anneal”, “hybridize” or “bind,” generally refer to thecombining of one or more single-stranded polynucleotide sequences,segments or strands, and allowing them to form a double-strandedmolecule through base pairing. Two complementary sequences (e.g.,ribonucleic acid (RNA) and/or deoxyribonucleic acid (DNA)) can anneal orhybridize by forming hydrogen bonds with complementary bases to producea double-stranded polynucleotide or a double-stranded region of apolynucleotide.

As used herein the term “incorporating” when used with respect to theincorporation of an adapter may refer to the physical attachment of theadapter, to an extension of said adapter, or to the generation of asequence that is complementary to an adaptor sequence in a nucleic acidmolecule.

The term “subject” can be any animal which may benefit from the methodsof the disclosure, including, e.g., humans and non-human mammals, suchas primates, rodents, horses, dogs and cats. Subjects include withoutlimitation a eukaryotic organism, a mammal such as a primate, e.g.,chimpanzee or human, cow; dog; cat; a rodent, e.g., guinea pig, rat,mouse; rabbit; or a bird; reptile; or fish. Subjects specificallyintended for treatment using the methods described herein includehumans. A subject may be an individual or a patient.

As used herein, the term “primer extension reaction” generally refers tothe denaturing of a double-stranded nucleic acid, binding of a primer toone or both strands of the denatured nucleic acid, followed byelongation of the primer(s).

As used herein, the term “reaction mixture” generally refers to acomposition comprising reagents necessary to complete nucleic acidamplification (e.g., DNA amplification, RNA amplification), withnon-limiting examples of such reagents that include primer sets havingspecificity for target RNA or target DNA, DNA produced from reversetranscription of RNA, a DNA polymerase, a reverse transcriptase (e.g.,for reverse transcription of RNA), suitable buffers (includingzwitterionic buffers), co-factors (e.g., divalent and monovalentcations), dNTPs, and other enzymes (e.g., uracil-DNA glycosylase (UNG)),etc). In some cases, reaction mixtures can also comprise one or morereporter agents.

As used herein, a “reporter agent” generally refers to a compositionthat yields a detectable signal, the presence or absence of which can beused to detect the presence of amplified product.

As used herein, the term “target nucleic acid” generally refers to anucleic acid molecule in a starting population of nucleic acid moleculeshaving a nucleotide sequence whose presence, amount, and/or sequence, orchanges in one or more of these, are desired to be determined. A targetnucleic acid may be any type of nucleic acid, including DNA, RNA, andanalogues thereof.

The terms “polynucleotides”, “nucleic acid”, “nucleotides” and“oligonucleotides” can be used interchangeably. They can refer to apolymeric form of nucleotides of any length, either deoxyribonucleotidesor ribonucleotides, fragments, or analogs thereof. The following arenon-limiting examples of polynucleotides: coding or non-coding regionsof a gene or gene fragment, loci (locus) defined from linkage analysis,exons, introns, messenger RNA (mRNA), transfer RNA, transfer-messengerRNA, ribosomal RNA, antisense RNA, small nuclear RNA (snRNA), smallnucleolar RNA (snoRNA), micro-RNA (miRNA), small interfering RNA(siRNA), ribozymes, cDNA, recombinant polynucleotides, branchedpolynucleotides, plasmids, vectors, isolated DNA of any sequence,isolated RNA of any sequence, nucleic acid probes, and primers.

A polynucleotide may comprise modified nucleotides, such as methylatednucleotides and nucleotide analogues. If present, modifications to thenucleotide structure may be imparted before or after assembly of thepolymer. The sequence of nucleotides may be interrupted bynon-nucleotide components. A polynucleotide may be further modifiedafter polymerization, such as by conjugation with a labeling component.A nucleic acid described herein can contain phosphodiester bonds. Insome instances, the nucleic acids can be DNA (including, e.g., genomicDNA, mitochondrial DNA, and cDNA), RNA (including, e.g., mRNA and rRNA)or a hybrid, where the nucleic acid contains any combination ofdeoxyribo- and ribo-nucleotides, and any combination of bases, includinguracil, adenine, thymine, cytosine, guanine, inosine, xathaninehypoxathanine, isocytosine, isoguanine, etc. A polynucleotide isintended to encompass a singular nucleic acid as well as plural nucleicacids. The polynucleotide may be composed of any polyribonucleotide orpolydeoxyribonucleotide, which may be unmodified RNA or DNA or modifiedRNA or DNA. For example, polynucleotides may be composed of single- anddouble-stranded DNA, DNA that is a mixture of single- anddouble-stranded regions, single- and double-stranded RNA, and RNA thatis mixture of single- and double-stranded regions, hybrid moleculescomprising DNA and RNA that may be single-stranded or, more typically,double-stranded or a mixture of single- and double-stranded regions.

The term “primer”, as used herein, refers to an oligonucleotide,occurring naturally as in a purified restriction digest or producedsynthetically that is characterized by an ability to be extended againsta template oligonucleotide, so that an oligonucleotide whose sequence iscomplementary to that of at least a portion of the template molecule islinked to the primer, when all are placed in the presence of nucleotidesat a suitable temperature and pH. However, the mere ability to be usedin this fashion does not require that primers be fully extended againsta template, and in some instances, primers are used only as a site forthe addition of a small number of non-templated nucleotides. Primerssuch as primer hexamers having a length of at least 6 nucleotides longcan be used. In some instances, a primer may be fluorescently labeled(e.g., 5′-/56FAM/TGATGACGAGGCATTTGGC/3′). In some instances, primershave a length within the range of about 6 to about 100 nucleotides, orin some instances from about 10 to about 70 nucleotides. In someinstances, larger primers can be used. In some instances, random primersmay be used. In some instances, a primer may be a random primer. In someinstances, one or more primer(s) may be one or more random primer(s).

The term “one or more primer(s)” can comprise any number of primers orrandom primers. For example, “one or more primer(s)” can include atleast, at most, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 20, 31, 32,33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50,51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68,69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86,87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, or 100 primers orrandom primers. One or more primer(s) can include about 1 to about 2,about 1 to about 3, about 1 to about 4, about 1 to about 5, about 1 toabout 6, about 1 to about 7, about 1 to about 8, about 1 to about 9,about 1 to about 10, about 1 to about 15, about 1 to about 20, about 1to about 25, about 1 to about 30, about 1 to about 35, about 5 to about15, about 3 to about 10, about 5 to about 20, about 10 to about 50,about 30 to about 100, or more than about 100 primers. One or moreprimer(s) can comprise any number of primers.

The term “random primer,” as used herein, refers to a primer containinga random base sequence therein, and is intended to encompass primerswhether they consist partially or wholly of random base sequences.

As used herein, “homologue” refers to a protein that is functionallyequivalent i.e. has the same enzymatic activity as an enzyme having anamino acid sequence of the specified sequence identification number, butmay have a limited number of amino acid substitutions, deletions,insertions or additions in the amino acid sequence. In order to maintainthe function of the protein, the substitutions may be conservativesubstitutions, replacing an amino acid with one having similarproperties.

The term “heterologous” refers to a molecule or activity derived from asource other than the referenced species whereas “homologous” refers toa molecule or activity derived from the host microbial organism.Accordingly, exogenous expression of an encoding nucleic acid of thepresent disclosure may use either or both a heterologous or homologousencoding nucleic acid.

The tem “acceptor template,” as used herein, generally refers to anucleic acid molecule that is used to synthesize complementary DNA(cDNA) molecules. The acceptor nucleic acid may be modified. Theacceptor nucleic acid molecule may be modified at the 3′ end, forexample to protect it from being mistaken as an RNA primer. Themodification of the acceptor nucleic acid molecule may comprise adideoxy 3′ end. The modification may comprise a phosphorylated 3′ end.In some instances, the phosphorylated 3′ end of a polynucleotide or ofan acceptor nucleic acid molecule, which typically has a hydroxyl groupon its 3′ end, can act as a 3′ block because extension by an enzyme ofthe present disclosure, or of DNA polymerase for example may beinhibited or ligation by a ligase may be inhibited. Another non-limitingexample of a 3′ block includes the addition of a 3′ C3 spacer(three-carbon spacer) to the 3′ end of a polynucleotide which canfunction as an effective blocking agent against polymerase extension.Zhou, et al., Clin. Chem., 50: 1328-1335 (2004). Thus, the 3′ end can beblocked by the addition of, for example, a C3 spacer, a phosphate, anamine group (NH2), or any other chemical modification that inhibitsformation of a subsequent phosphodiester bond between the 3′ end of thepolynucleotide and another nucleotide.

An “overhang sequence,” as used herein, generally refers to a singlestranded region of nucleic acid extending from a double stranded region.

An “isolated” polynucleotide, as used herein, generally refers apolynucleotide that has been either removed from its naturalenvironment, produced using recombinant techniques, or chemically orenzymatically synthesized. A polynucleotide can also be purified, i.e.,essentially free from any other polynucleotides and associated cellularproducts or other impurities.

The term “polymerase” as used herein, generally refers to an enzyme thatlinks individual nucleotides together into a strand, using anotherstrand as a template. In some instances, the polymerase is a polymerasewith editing capabilities. In some instances, the polymerase withediting capabilities may be 3′ to 5′ exonuclease, T4 DNA polymerase,exonuclease I, Phi29, Pfu, Vent, KOD, exonuclease III, and exonucleaseT. Examples of polymerases can include a DNA polymerase, an RNApolymerase, an RNA-directed DNA polymerase, reverse transcriptase, apolypeptide having reverse transcriptase activity, or any variantthereof, a thermostable polymerase, a wild-type polymerase, a modifiedpolymerase, E. coli DNA polymerase I, T7 DNA polymerase, bacteriophageT4 DNA polymerase PHI 29 (phi29) DNA polymerase, Taq polymerase, Tthpolymerase, Tli polymerase, Pfu polymerase VENT polymerase, DEEPVENTpolymerase, EX-Taq polymerase, LA-Taq polymerase, Sso polymerase, Pocpolymerase, Pab polymerase, Mth polymerase, ES4 polymerase, Trupolymerase, Tac polymerase, Tne polymerase, Tma polymerase, Tcapolymerase, Tih polymerase, Tfi polymerase, Platinum Taq polymerases,Tbr polymerase, Tfl polymerase, Tth polymerase, Pfutubo polymerase,Pyrobest polymerase, Pwo polymerase, KOD polymerase, Bst polymerase, Sacpolymerase, Klenow fragment, polymerase with 3′ to 5′ exonucleaseactivity, and variants, modified products and derivatives thereof. Insome instances, the polymerase may be a reverse transcriptase or amodified reverse transcriptase of the present disclosure. In someinstances, the polymerase is a single subunit polymerase. The polymerasecan have high processivity, namely the capability of the polymerase toconsecutively incorporate nucleotides into a nucleic acid templatewithout releasing the nucleic acid template. In some cases a polymerasecan be a polymerase described in PCT/US2017/061197, such as P2.PCT/US2017/061197 is incorporated herein in its entirety.

The term “reverse transcriptase” or RT, as used herein, generally refersto an enzyme with both an RNA-directed DNA polymerase and a DNA-directedDNA polymerase. RT refers to a group of enzymes having reversetranscriptase activity (e.g., that catalyze synthesis of DNA from an RNAtemplate). In general, such enzymes include, but are not limited to,retroviral reverse transcriptase, retrotransposon reverse transcriptase,retroplasmid reverse transcriptases, retron reverse transcriptases,bacterial reverse transcriptases, group II intron-derived reversetranscriptase, and mutants, variants or derivatives thereof.Non-retroviral reverse transcriptases include non-long terminal repeat(LTR) retrotransposon reverse transcriptases, retroplasmid reversetranscriptases, retron reverse transcriptases, and group II intronreverse transcriptases. Further bacterial reverse transcriptases aredescribed by Simon D & Zimmerly S (2008) “A diversity of uncharacterizedretroelements in bacteria” Nucleic Acids Res 36(22):7219-7229., andKojima, K K & Kanehisa, M (2008) “Systematic survey for novel types ofprokaryotic retroelements based on gene neighborhood and proteinarchitecture” Mol Biol Evol 25:1395-1404, which describe many classes ofnon-retroviral reverse transcriptases (i.e., retrons, group II introns,and diversity-generating retroelements among others). Reversetranscriptase has been used primarily to transcribe RNA into cDNA, whichcan then be cloned into a vector for further manipulation or used invarious amplification methods such as polymerase chain reaction, nucleicacid sequence-based amplification (NASBA), transcription mediatedamplification (TMA), self-sustained sequence replication (3SR), diverseprimer extension reactions, 5′RACE, detection of chemical modificationsor other techniques that require synthesis of DNA using an RNA template.

Reverse Transcriptases

Reverse transcriptase enzymes may be isolated from a large number ofmobile genetic elements which are of retroviral and non-retroviralorigin. Such mobile genetic elements are resident in the genomes ofhigher order species and play a function role in life cycle of thesemobile genetic elements. Mobile genetic elements may encode genes forreverse transcriptase enzymes (reviewed in Howard M Temin, ReverseTranscription in the Eukaryotic Genome: Retroviruses. Pararetroviruses,Retrotransposons, and Retrotranscripts, Mol. Biol. Evol. 2(6):455-468).These elements include, but are not limited, to retrotransposons.Retrotransposons include the non-long terminal repeat (LTR)retrotransposon and LTR mobile elements (e.g., TY3, TY5, non-LTR,LINE-L1, R2, R1). (Reviewed by Cordaux and Batzer, Nature Reviews,October 2009, volume 10, pp 691-703).

Retroelements, genetic elements that encode RTs, are divided into twomajor families denoted LTR-containing retroelements andnon-LTR-containing retroelements (Xiong Y, Eickbush T H (1990) “Originand evolution of retroelements based upon their reverse transcriptasesequences” EMBO J 9:3353-62). Non-LTR-retroelements are a diverse familyof RT-encoding elements that includes retroplasmids,non-LTR-retrotransposons, retrons, and mobile group II introns.

The mutants of the present disclosure may be generated in accordancewith any suitable method, including, but not limited to, methodsdescribed and exemplified herein. Mutations, such as substitutions,insertions, deletions, and/or side chain modifications, may beintroduced into the nucleotide and amino acid sequences of the gene ofinterest using any suitable technique, including site-directedmutagenesis (Wu, ed., Meth. Enzymol. 217, Academic Press (1993)). Thelambda red recombinase method may be used to “knock out” genes (Datsenkoet al., PNAS USA 97: 6640-6645 (2000)). Permanent, marker-free, multiplegene disruptions may be created.

Non-Naturally Occurring Nucleotides and Amino Acids Also May be Used.

Methods of Expressing Non-Naturally Occurring Enzymes from a Host SystemNon-naturally occurring enzymes, including R2 enzymes, can be difficultto manufacture, in part because of their size, structural complexity,and amino acid composition. In addition, R2 retroelements aremulti-domain elements with molecular masses usually over 100 kD, whichincreases the challenges in manufacturing R2 enzymes recombinantly.Furthermore, naturally occurring R2 enzymes need to be expressed at lowlevels in host organisms largely because of their toxic effects to thehost. In addition, naturally occurring R2 retroelements are believed tofunction as dimers.

In some aspects, the disclosure provides recombinantly manufacturedenzymes comprising select sequences derived from an R2 retrotransposonand vectors comprising a nucleic acid sequence encoding therecombinantly manufactured enzymes disclosed herein. R2 retroelementsare usually composed of three major domains (FIG. 1A, 1B, 1C): anN-terminal domain, a reverse transcriptase domain, and an endonucleasedomain. The N-terminal domain may include zinc-finger and c-myb DNAbinding motifs, which are believed to contribute to specific recognitionand binding to target DNA (target primed reverse transcription mechanism(TPRT). The reverse transcriptase domain is responsible for copying R2RNA template. Lastly, the endonuclease domain is responsible forspecific cleavage of target DNA.

In some aspects, the disclosure provides non-naturally occurring enzymesthat are phylogenetically related to one or more elements of an R2retroelement. In some instances, the enzymes of the disclosure do notcomprise the N-terminal domain of an R2 enzyme. In some aspects, thedisclosure provides a method for generating a non-naturally occurringenzyme comprising: expressing a heterologous sequence encoding saidnon-naturally occurring enzyme in a host, wherein said non-naturallyoccurring enzyme comprises a first, a second, and a third domain derivedfrom an R2 retrotransposon; such as for example, a palm, a finger, and athumb domain derived from an R2 retrotransposon; an endonuclease domainderived from an R2 retrotransposon; and purifying said non-naturallyoccurring enzyme from said host, thereby generating said non-naturallyoccurring enzyme.

In some aspects, the disclosure provides non-naturally occurring enzymeswhereby the N-terminal domain is removed. The N-terminal domain isbelieved to interfere with the expression and stability of R2retroelements. As such, the removal of parts of the entire N-terminal orparts of the N-terminal is believed to improve the expression andstability of the R2 retroelement without necessarily affecting thedisclosed enzyme's ability and performance in RNA library preparationfor sequencing. In some aspects, the disclosure identifies the saidN-terminal domain using sequence analysis of the R2 retrotransposon andother phylogenetically related R2 retroelements. In some instances, theenzyme of the disclosure is an enzyme that is phylogenetically relatedto one or more elements of an R2 retroelement and in some instances, theN-terminal domain is removed from said enzyme.

In some aspects, the disclosure provides non-naturally occurring enzymescomprising fusion-tag molecules, whereby the fusion-tag moleculestabilizes the non-naturally occurring enzymes disclosed herein. In someaspects, the fusion-tag molecules are selected from the group consistingof: Fh8, MBP, NusA, Trx, SUMO, GST, SET, GB1, ZZ, HaloTag, SNUT, Skp,T7PK, EspA, Mocr, Ecotin, CaBP, ArsC, IF2-domain I, an IF2-domain Iderived tag, RpoA, SlyD, Tsf, RpoS, PotD, Crr, msyB, yjgD, rpoD, andHis6.

In some aspects, the disclosure provides non-naturally occurring enzymescomprising fusion-tag molecules, whereby the fusion-tag moleculestabilizes the non-naturally occurring enzymes disclosed herein. In someaspects, the fusion-tag molecules are selected from the group consistingof: His-tag, His6-tag, Calmodulin-tag, CBP, CYD (covalent yetdissociable NorpD peptide), Strep II, FLAG-tag, HA-tag, Myc-tag, S-tag,SBP-tag, Softag-1, Softag-3, V5-tag, Xpress-tag, Isopeptag, SpyTag, B,HPC (heavy chain of protein C) peptide tags, GST, MBP, biotin, biotincarboxyl carrier protein, glutathione-S-transferase-tag, greenfluorescent protein-tag, maltose binding protein-tag, Nus-tag,Strep-tag, and thioredoxin-tag.

In some aspects, the disclosure provides non-naturally occurringenzymes, whereby at least one of said palm and finger domain from an R2retrotransposon, said thumb domain of an R2 retrotransposon, or saidendonuclease domain of an R2 retrotransposon are derived from anarthropod.

In some aspects, the disclosure provides non-naturally occurringenzymes, whereby at least one of said palm and finger domain from an R2retrotransposon, said thumb domain of an R2 retrotransposon, or saidendonuclease domain of an R2 retrotransposon is derived from silkmoth.

In some aspects, the disclosure provides non-naturally occurringenzymes, whereby at least one of said palm and finger domain from an R2retrotransposon, said thumb domain of an R2 retrotransposon, or saidendonuclease domain of an R2 retrotransposon is derived from avertebrate or an echinoderm.

In some aspects, the disclosure provides non-naturally occurringenzymes, whereby at least one of said palm and finger domain from an R2retrotransposon, said thumb domain of an R2 retrotransposon, or saidendonuclease domain of an R2 retrotransposon is derived from a flatwormor a hydra.

In some aspects, the disclosure provides non-naturally occurring enzymeswith at least 80% identify to SEQ ID Nos: 1-20, with at least 81%identify to SEQ ID Nos: 1-20, with at least 82% identify to SEQ ID Nos:1-20, with at least 83% identify to SEQ ID Nos: 1-20, with at least 84%identify to SEQ ID Nos: 1-20, with at least 85% identify to SEQ ID Nos:1-20, with at least 86% identify to SEQ ID Nos: 1-20, with at least 87%identify to SEQ ID Nos: 1-20, with at least 88% identify to SEQ ID Nos:1-20, with at least 89% identify to SEQ ID Nos: 1-20, with at least 90%identify to SEQ ID Nos: 1-20, with at least 91% identify to SEQ ID Nos:1-20, with at least 92% identify to SEQ ID Nos: 1-20, with at least 93%identify to SEQ ID Nos: 1-20, with at least 94% identify to SEQ ID Nos:1-20, with at least 95% identify to SEQ ID Nos: 1-20, with at least 96%identify to SEQ ID Nos: 1-20, with at least 97% identify to SEQ ID Nos:1-20, with at least 98% identify to SEQ ID Nos: 1-20, with at least 99%identify to SEQ ID Nos: 1-20, with at least 100% identify to SEQ ID Nos:1-20.

In some aspects, the disclosure provides non-naturally occurring enzymeswherein the host is selected from bacteria, yeast, algae, cyanobacteria,fungi, a plant cell, or any combination thereof. In some instances, thedisclosure provides non-naturally occurring enzymes wherein the host isE. coli.

In some aspects, the disclosure provides a non-naturally occurringenzyme, which can comprise one or more amino acid mutations in motif-1,motif-0, and the thumb subunit (FIGS. 2, 3, and 4 ). Suitable amino acidmodifications for improving a property of an R2 related enzyme can beconservative or non-conservative mutations. In some instances, motif-1and motif-0 can be present in non-long terminal repeat (LTR)retrotransposons and telomerase, but not retroviral transposons and LTRretroelements. A mutation can be made such that the encoded amino acidis modified to a polar, non-polar, basic or acidic amino acid. FIGS. 15and 16 disclose potential mutations in motif-1 or motif-0 that canimprove one or more properties of an R2 enzyme derived from silkmoth,whereby the silkmoth R2 reference sequence is disclosed in FIG. 14 . Forinstance, the following amino acid substitutions may be engineered inmotif-1: A15→V15, A15→M15, A17→V17, A17→M17, H18→V18, H18→N18, R22→K22,R22→H22, Q23→I23, Q23→E23, K24→A24, K24→I24, K24→R24, R25→K25, R26→K26,R26→T26, R26→D26, A27→M27, A27→I27, A27→Q27, E28→D28, E28→Q28, Y29→I29,Y29→F29, A30→S30, A30→R30, R31→K31, R31→A31, V32→T32, V32ΘM32, V32→F32,Q33→N33, E34→Q34, E34→R34, E34→D34, L35→F35, L35→A35, Y36→F36, Y36→W36,K37→R37, K37→H37, K38→R38, K38→T38, C39→D39, C39→N39, R40→M40, R40→I40,R40→K40, S41→T41, S41→Q41, R42→Q42, R42→K42, R42→A42, A43→C43, A43→L43,A44→I44, A44→V44, A45→H45, A45→R45, E46→R46, E46→K46, E46→D46, V47→L47,V47→I47, I48→L48, I48→F48, D49→G49, D49→S49, D49→E49, G50→A50, G50→E50,G50→K50, A51→T51, A51→D51, C52→A52, C52→T52, G53→S53, G53→D53, G54→S54,G54→D54, V55→L55, V55→A55, G56→S56, G56→A56, M62→L62, M62→A62, Y65→F65,Y65→G65, W66→F66, W66→H66, I69→M69, I69→T69, L70→V70, L70→M70, V73→A73,V73→F73, S74→E74, S74→K74.

In some aspects, the disclosure provides a non-naturally occurringenzyme, which can comprise one or more amino acid mutations in motif-1,motif-0, and the thumb subunit (FIGS. 2, 3, and 4 ). A mutation can bemade such that the encoded amino acid is modified to a polar, non-polar,basic or acidic amino acid. FIG. 16 discloses potential mutations inmotif-0 that can improve one or more properties of an R2 enzyme derivedfrom silkmoth, whereby the silkmoth R2 reference sequence is disclosedin FIG. 14 . In some instances, the following amino acid substitutionsmay be engineered in motif-0: Q101→N101, Q101→S101, L102→V102,L102→I102, W103→M103, W103→V103, K104→R104, K104→S104, K104→D104,P105→A105, I106→L106, I106→V106, S107→T107, S107→V107, V108→N108,V108→L108, V108→S108, E109→D109, E109→Q109, E109→L109, E110→D110,I111→V111, I111→M111, K112→I1112, K112→R112, R115→H115, F116-L116,F116→A116, D117→C117, D117→S117, D117→E117, R119→T119, R119→N119,T120→S120, S121→A121, P122→A122, G123→A123, P124→L124, D125→N125,D125→E125, G126→S126, G126→K126, I127→M127, I127→V127, R128→T128,R128→K128, S129→L129, S129→H129, G130→K130, G130→S130, Q131→D131,Q131→R131, W132→L132, W132→A132, R133→N133, R133→Y133, R133→K133,A134→L134, A134→M134, V135→T135, V135→S135, P136→S136, V137→A137,V137→Q137, H138→I138, H138→A138, L139→A139, L139→M139, L139→V139,K140→R140, K140→N140, K140→L140, A141→deletion, E142→S142, E142→K142,E142→D142, M143→I143, M143→V143, F144→L144, F144→Y144, N145→D145,A146→L146, A146→V146, W147→F147, W147→L147, M148→L148, M148→V148,A149→L149, A149→F149, R150→T150, R150→H150, R150→K150, G151→R151,G151→E151, E152→R152, E152→N152, E152→D152, I153→V153, I153→C153,P154→A154, E155→K155, E155→P155, E155→Q155, E155→A155, E155→D155,I156→E156, I156→R156, I156→V156, L157→V157, L157→F157, R158→K158,R158→L158, R158→K158, Q159→L159, Q159→M159, Q159→H159, Q159→N159,C160→G160, C160→S160, C160→H160, R161→K161.

In some aspects, the disclosure provides a non-naturally occurringenzyme, which can comprise one or more amino acid mutations in motif-1,motif-0, and the thumb subunit (FIGS. 2 and 3 ). A mutation can be madesuch that the encoded amino acid is modified to a polar, non-polar,basic or acidic amino acid. FIG. 17 discloses potential mutations in thethumb subunit that can improve one or more properties of an R2 enzymederived from silkmoth, whereby the silkmoth R2 reference sequence isdisclosed in FIG. 14 . In some instances, the following amino acidsubstitutions may be engineered in the thumb subunit: G403→D403,G403→S403, G404→D404, G404→R404, G404→S404, K405→Q405, K405→V405,K405→R405, P406→V406, P406→Q406, P406→K406, L407→V407, L407→M407,R408→G408, R408→P408, R408→H408, R408→T408, R408→K408, Q409→A409,Q409→E409, Q409→S409, V410→M410, V410→L410, S411→D411, S411→G411,S411→K411, C412→I412, C412→H412, C412→A412, C412→R412, V413→E413,V413→L413, V413→A413, V413→G413, E414→G414, E414→H414, E414→Q414,E414→K414, W416→Y416, W416→V416, W416→F416, R417→K417, R417→H417,R417→T417, R417→G417, Y418→F418, L419→V419, L419→I419, G420→A420,V421→I421, V421→A421, V421→H421, D422→R422, D422→W422, D422→N422,D422→T422, D422→P422, D422→E422, F423→V423, F423→Y423, F423→I423,E424→G424, E424→A424, E424→N424, E424→R424, E424→T424, E424→S424,E424→D424, A425→S425, A425→H425, A425→G425, S426→T426, S426→A426,S426→E426, G427→A427, C428→T428, C428→P428, C428→R428, C428→C428→M428,V429→C429, V429→I429, V429→E429, V429→A429, T430→I430, T430→D430,T430→Q430, T430→R430, T430→T430→H430, S434→E434, S434→N434, I435→V435,I435→L435, I435→M435, S436→M436, S436→L436, S436→A436, S436→D436,S436→K436, S437→P437, S437→G437, S437→A437, S437→D437, S437→T437,A438→L438, A438→G438, A438→K438, A438→D438, A438→L438, L439→I439,L439→V439, N440→E440, N440→D440, N440→Q440, N440→K440, N441→E441,N441→R441, N441→A441, N441→Q441, I442→T442, I442→V442, S443→T443,S443→K443, S443→Q443, R444→A444, R444→C444, R444→S444, R444→Q444,R444→K444, A445→G445, A445→S445, P446→G446, L447→I447, K448→R448,P449→L449, Q450→E450, Q450→H450, Q451→E451, Q451→H451, L453→V453,L453→M453, E454→K454, E454→H454, E454→F454, E454→A454, E454→D454,I455→L455, I455→M455, I455→A455, L456→I456, R457→C457, R457→G457,R457→N457, R457→R457→K457, A458→N458, A458→T458, A458→V458, A458→S458,H459→Y459, H459→F459, H459→V459, L460→F460, L460→V460, I461→L461,I461→V461, P462→G462, R463→K463, R463→Q463, R463→G463, F464→Y464,F464→S464, F464→A464, F464→H464, Q465→T465, Q465→Y465, H466→Y466,H466→F466, G467→N467, G467→I467, G467→K467, G467→A467, F468→L468,F468→W468, V469→T469, V469→A469, V469→S469, V469→L469, L470→F470,L470→M470, L470→T470, G471→S471, G471→T471, G471→A471, N472→R472,N472→S472, N472→G472, R477→L477, R477→M477, R477→D477, R477→K477,L478→V478, L478→A478, R479→N479, R479→K479, R479→C479, R479→L479,R479→W479, M480→Q480, M480→K480, M480→T480, M480→R480, L481→G481,L481→T481, L481→M481, D482→N482, D482→E482, V483→S483, V483→K483,V483→R483, V483→L483, Q484→A484, Q484→I484, Q484→V484, Q484→M484,I485→T485, I485→V485, R486→K486, R486→L486, K487→A487, K487→T487,K487→Q487, K487→G487, K487→V487, K487→R487, A488→H488, A488→T488,A488→Y488, A488→S488, G490→R490, G490→K490, Q491→R491, Q491→T491,Q491→K491.

In some aspects, the mutagenized motif-1 sequence has an improvedjumping activity compared to the wild-type sequence. In some aspects,the mutagenized motif-0 sequence has an improved jumping activitycompared to the wild-type sequences. In some aspects, the mutagenizedthumb domain sequence has an improved single-stranded priming efficiencycompared to the wild-type sequences. In some instances, the mutagenizedthumb domain sequence has an improved processivity compared to thewild-type sequences. Jumping efficiency, single-stranded primingefficiency, and processivity are essential parameters for the conversionefficiency of RNA samples to DNA library.

In some instances, a host cell may be selected from, and the modified ornon-naturally occurring enzyme generated in, for example, bacteria,yeast, fungus or any of a variety of other organisms may be used as ahost organism.

In some instances, the host is not particularly restricted and theenzymatic activity or activities may be incorporated into any suitablehost organism using methods, for example, as described herein. In someinstances, the host is selected from bacteria, yeast, algae,cyanobacteria, fungi, or a plant cell, or any combination thereof. E.coli and S. cerevisiae are particularly useful host organisms since theyare well characterized microorganisms suitable for genetic engineering.In some instances, the host is E. coli.

Each of the enzymes described herein may be attached to an additionalamino acid sequence as long as it retains an activity functionallyequivalent to that of the enzyme. As mentioned above, it is understoodthat each enzyme or a homologue thereof may be a (poly)peptide fragmentas long as it retains an activity functionally equivalent to that of theenzyme.

In some instances, the enzyme is selected and/or engineered to exhibithigh fidelity with low error rates. The fidelity of a nucleotidepolymerase is typically measured as the error rate, i.e., the frequencyof incorporation of a nucleotide in a manner that may violate the widelyknown Watson-Crick base pairing rules. The fidelity or error rate of apolymerase (e.g., DNA polymerase) may be measured using any suitableassay. See, for example, Lundburg et al., 1991 Gene, 108:1-6. The term“fidelity” can be used to refer to the accuracy of polymerization, orthe ability of the polymerase to discriminate correct from incorrectsubstrates, (e. g., nucleotides) when synthesizing nucleic acidmolecules (e. g. RNA or DNA) which are complementary to a template. Thehigher the fidelity of an enzyme, the less the enzyme misincorporatesnucleotides in the growing strand during nucleic acid synthesis; thatis, an increase or enhancement in fidelity results in a more faithfulpolymerase having decreased error rate (decreased misincorporationrate). In some instances, the misincorporation error rate is at mostabout 10-2, 10-4, 10-6, or 10-8.

In some aspects, the present disclosure relates to a non-naturallyoccurring or modified enzyme that can be readily expressed in arecombinant system in a functional form. In some instances, thenon-naturally occurring or modified enzyme is an enzyme with reversetranscriptase activity. In some instances, the non-naturally occurringor modified enzyme is a modified reverse transcriptase. In someinstances, the non-naturally occurring or modified enzyme is a modifiednon-retroviral reverse transcriptase. In some instances, thenon-naturally occurring or modified enzyme is a modified non-LTRretrotransposon. In some instances, the non-naturally occurring ormodified enzyme is a modified R2 reverse transcriptase, comprisingmutations in an R2 Motif-1 or Motif-0. In some instances, anon-naturally occurring or modified enzyme or a modified polypeptidehaving reverse transcriptase activity can amplify a template nucleicacid molecule at a processivity of at least about 80% per base, of atleast 81% per base, of at least 82% per base, of at least 83% per base,of at least 84% per base, of at least about 85% per base, of at least86% per base, of at least 87% per base, of at least about 88% per base,of at least about 89% per base, of at least about 90% per base, of atleast about 91% per base, of at least about 92% per base, of at leastabout 93% per base, of at least about 94% per base, of at least about95% per base, of at least about 96% per base, of at least about 97% perbase, of at least about 98% per base, of at least about 99% per base, ofat least about 99.5% per base, or of about 100% per base.

In some instances, a non-naturally occurring or modified enzyme or amodified polypeptide having reverse transcriptase activity can amplifyor is capable of amplifying a template nucleic acid molecule at aprocessivity measured at a temperature of between about 12° C. and about40° C. In some instances, the temperature is between about 10° C. andabout 35° C., between about 12° C. and about 30° C., between about 25°C. and about 40° C., or between about 12° C. and about 42° C. In someinstances, the temperature is between about 8° C. to about 50° C.,between about 2° C. to about 60° C., between about 8° C. to about 42°C., between about 6° C. to about 32° C., or between about 7° C. to about35° C.

In some instances, a non-naturally occurring or modified enzyme or amodified polypeptide having reverse transcriptase activity can amplifyor is capable of amplifying a template nucleic acid molecule at aprocessivity of at least about 80% per base at a temperature at about orat most about 4° C., at about or at most about 8° C., at about or atmost about 12° C., at about or at most about 15° C., at about or at mostabout 20° C., at about or at most about 25° C., at about or at mostabout 30° C., at about or at most about 35° C., at about or at mostabout 40° C., or at about or at most about 42° C.; of at least about 85%per base at a temperature of about or at most about 12° C., at about orat most about 15° C., at about or at most about 20° C., at about or atmost about 25° C., at about or at most about 30° C., at about or at mostabout 35° C., at about or at most about 40° C., at about or at mostabout 42° C., at about or at most about 45° C., at about or at mostabout 50° C.; of at least about 89% per base at a temperature at aboutor at most about 4° C., at about or at most about 8° C., at about or atmost about 12° C., at about or at most about 15° C., at about or at mostabout 20° C., at about or at most about 25° C., at about or at mostabout 30° C., at about or at most about 35° C., at about or at mostabout 40° C., or at about or at most about 42° C.; of at least about 90%per base at a temperature of about or at most about 12° C., at about orat most about 15° C., at about or at most about 20° C., at about or atmost about 25° C., at about or at most about 30° C., at about or at mostabout 35° C., at about or at most about 40° C., at about or at mostabout 42° C., at about or at most about 45° C., at about or at mostabout 50° C.; of at least about 91% per base at a temperature at aboutor at most about 4° C., at about or at most about 8° C., at about or atmost about 12° C., at about or at most about 15° C., at about or at mostabout 20° C., at about or at most about 25° C., at about or at mostabout 30° C., at about or at most about 35° C., at about or at mostabout 40° C., or at about or at most about 42° C.; of at least about 85%per base at a temperature of about or at most about 12° C., at about orat most about 15° C., at about or at most about 20° C., at about or atmost about 25° C., at about or at most about 30° C., at about or at mostabout 35° C., at about or at most about 40° C., at about or at mostabout 42° C., at about or at most about 45° C., at about or at mostabout 50° C.; of at least about 95% per base at a temperature at aboutor at most about 4° C., at about or at most about 8° C., at about or atmost about 12° C., at about or at most about 15° C., at about or at mostabout 20° C., at about or at most about 25° C., at about or at mostabout 30° C., at about or at most about 35° C., at about or at mostabout 40° C., or at about or at most about 42° C.; of at least about 85%per base at a temperature of about or at most about 12° C., at about orat most about 15° C., at about or at most about 20° C., at about or atmost about 25° C., at about or at most about 30° C., at about or at mostabout 35° C., at about or at most about 40° C., at about or at mostabout 42° C., at about or at most about 45° C., at about or at mostabout 50° C.; of at least about 99% per base at a temperature at aboutor at most about 4° C., at about or at most about 8° C., at about or atmost about 12° C., at about or at most about 15° C., at about or at mostabout 20° C., at about or at most about 25° C., at about or at mostabout 30° C., at about or at most about 35° C., at about or at mostabout 40° C., or at about or at most about 42° C.; of at least about 85%per base at a temperature of about or at most about 12° C., at about orat most about 15° C., at about or at most about 20° C., at about or atmost about 25° C., at about or at most about 30° C., at about or at mostabout 35° C., at about or at most about 40° C., at about or at mostabout 42° C., at about or at most about 45° C., at about or at mostabout 50° C.; of at least about 99.5% per base at a temperature at aboutor at most about 4° C., at about or at most about 8° C., at about or atmost about 12° C., at about or at most about 15° C., at about or at mostabout 20° C., at about or at most about 25° C., at about or at mostabout 30° C., at about or at most about 35° C., at about or at mostabout 40° C., or at about or at most about 42° C.; of at least about 85%per base at a temperature of about or at most about 12° C., at about orat most about 15° C., at about or at most about 20° C., at about or atmost about 25° C., at about or at most about 30° C., at about or at mostabout 35° C., at about or at most about 40° C., at about or at mostabout 42° C., at about or at most about 45° C., at about or at mostabout 50° C.; or of about 100% per base at a temperature at about or atmost about 4° C., at about or at most about 8° C., at about or at mostabout 12° C., at about or at most about 15° C., at about or at mostabout 20° C., at about or at most about 25° C., at about or at mostabout 30° C., at about or at most about 35° C., at about or at mostabout 40° C., or at about or at most about 42° C.; of at least about 85%per base at a temperature of about or at most about 12° C., at about orat most about 15° C., at about or at most about 20° C., at about or atmost about 25° C., at about or at most about 30° C., at about or at mostabout 35° C., at about or at most about 40° C., at about or at mostabout 42° C., at about or at most about 45° C., at about or at mostabout 50° C.

In some instances, the non-naturally occurring or modified enzyme or amodified polypeptide having reverse transcriptase activity can amplifyor is capable of amplifying a template nucleic acid molecule at aprocessivity of at least about 80% per base at a temperature of at mostabout 35° C., of at least about 85% per base at a temperature of at mostabout 40° C., of at least about 88% per base at a temperature of at mostabout 35° C., of at least about 89% per base at a temperature of at mostabout 40° C., of at least about 90% per base at a temperature of at mostabout 35° C., of at least about 91% per base at a temperature of at mostabout 35° C., of at least about 92% per base at a temperature of at mostabout 40° C., of at least about 93% per base at a temperature of at mostabout 35° C., of at least about 94% per base at a temperature of at mostabout 40° C., of at least about 95% per base at a temperature of at mostabout 35° C., of at least about 96% per base at a temperature of at mostabout 40° C., of at least about 97% per base at a temperature of at mostabout 35° C., of at least about 98% per base at a temperature of at mostabout 40° C., of at least about 99% per base at a temperature of at mostabout 40° C., of at least about 99.5% per base at a temperature of atmost about 40° C., or of about 100% per base at a temperature of at mostabout 40° C.

In some instances, the improved enzyme property is selected from atleast one of the following: improved stability (e.g., improvedthermostability), improved specific activity, improved proteinexpression, improved purification, improved processivity, improvedstrand displacement, improved template jumping, improved DNA/RNAaffinity, improved single strand DNA priming, and improved fidelity. Insome instances, a non-naturally occurring enzyme or a modified enzyme ora modified polypeptide having reverse transcriptase activity amplifies atemplate nucleic acid molecule. In some instances, the non-naturallyoccurring enzyme or the modified enzyme or the modified polypeptidehaving reverse transcriptase activity that amplifies a template nucleicacid molecule has a performance index greater than about 1, greater thanabout 2, greater than about 3, greater than about 4, greater than about5, greater than about 6, greater than about 7, greater than about 8,greater than about 9, greater than about 10, greater than about 15,greater than about 20, greater than about 25, greater than about 30,greater than about 35, greater than about 40, greater than about 45,greater than about 50, greater than about 60, greater than about 70,greater than about 80, greater than about 90, or greater than about 100for at least one enzyme property. In some instances, the enzyme propertyand/or the performance index is performed at a temperature equal to orlower than or at most about 50° C., equal to or lower than or at mostabout 42° C., equal to or lower than or at most about 40° C., equal toor lower than or at most about 39° C., equal to or lower than or at mostabout 38° C., equal to or lower than or at most about 37° C., equal toor lower than or at most about 36° C., equal to or lower than or at mostabout 35° C., equal to or lower than or at most about 34° C., equal toor lower than or at most about 33° C., equal to or lower than or at mostabout 32° C., equal to or lower than or at most about 31° C., equal toor lower than or at most about 30° C., equal to or lower than or at mostabout 29° C., equal to or lower than or at most about 28° C., equal toor lower than or at most about 27° C., equal to or lower than or at mostabout 26° C., equal to or lower than or at most about 25° C., equal toor lower than or at most about 23° C., equal to or lower than or at mostabout 20° C., equal to or lower than or at most about 15° C., equal toor lower than or at most about 13° C., equal to or lower than or at mostabout 12° C., equal to or lower than or at most about 10° C., equal toor lower than or at most about 8° C., equal to or lower than or at mostabout 4° C. In some instances, the non-naturally occurring enzyme or themodified enzyme (e.g., modified reverse transcriptase) or the modifiedpolypeptide having reverse transcriptase activity exhibits aprocessivity for a given nucleotide substrate that is at least about 5%,at least about 10%, at least about 15%, at least about 20%, at leastabout 25%, at least about 30%, at least about 35%, at least about 37.5%,at least about 40%, at least about 45%, at least about 50%, at leastabout 60%, at least about 70%, at least about 75%, at least about 80%,at least about 90%, at least about 95%, at least about 100%, at leastabout 110%, at least about 125%, at least about 150%, at least about170%, at least about 190%, at least about 200%, at least about 250%, atleast about 500%, at least about 750%, at least about 1000%, at leastabout 5000%, or at least about 10000% higher than the processivity of areference enzyme or a reference polypeptide for the same nucleotidesubstrate. In some instances, the non-naturally occurring enzyme is anon-naturally occurring reverse transcriptase enzyme. In some instances,the modified enzyme is a modified reverse transcriptase.

The present disclosure relates to processes and/or methods that requireconsiderably less hands-on time, the protocol is much simpler to performand requires a much shorter duration time than other methods used forRNA sequencing and/or liquid biopsy, for example. In some instances, themethods and processes of the present disclosure comprises a protocolthat is less than about 2 hours and/or less than about 30 minutes ofhands-on time. In some instances, the protocol is less than about 20hours, less than about 15 hours, less than about 12 hours, less thanabout 11 hours, less than about 10 hours, less than about 9 hours, lessthan about 8 hours, less than about 7 hours, less than about 6 hours,less than about 5 hours, less than about 4 hours, less than about 3hours, less than about 2.5 hours, less than about 2 hours, less thanabout 1.5 hours, less than about 1 hour, or less than about 30 minutes.In some instances, the hands-on time is less than about 5 hours, lessthan about 4 hours, less than about 3 hours, less than about 2.5 hours,less than about 2 hours, less than about 1.5 hours, less than about 1hour, less than about 50 minutes, less than about 40 minutes, less thanabout 35 minutes, less than about 30 minutes, less than about 25minutes, less than about 20 minutes, or less than about 15 minutes.

In some aspects, the disclosure provides a method for simultaneouslyamplifying a messenger ribonucleic (mRNA) molecule and adeoxyribonucleic (DNA) molecule. In some instances, said methodcomprises providing a reaction mixture comprising said mRNA, DNA andnon-naturally occurring enzymes, each of said non-naturally occurringenzymes comprising (i) a palm and finger domain derived from an R2retrotransposon; (ii) a thumb domain derived from an R2 retrotransposon;and (iii) an endonuclease domain derived from an R2 retrotransposon. Insome instances, said method comprises subjecting said reaction mixtureto conditions sufficient to amplify said mRNA and DNA, thereby yieldingamplified products of said mRNA and said DNA. In some instances, saidDNA is complementary DNA derived from a subset of mRNA in said reactionmixture.

In some instances, the non-naturally occurring or modified enzyme (e.g.,non-naturally occurring or modified reverse transcriptase, non-naturallyoccurring or modified non-LTR retrotransposon, non-naturally occurringor modified R2 reverse transcriptase) or a modified polypeptide havingreverse transcriptase activity exhibits a misincorporation error rate ofequal to or less than about 50%, equal to or less than about 45%, equalto or less than about 40%, equal to or less than about 35%, equal to orless than about 30%, equal to or less than about 25%, equal to or lessthan about 20%, equal to or less than about 15%, equal to or less thanabout 10%, equal to or less than about 9%, equal to or less than about8%, equal to or less than about 7%, equal to or less than about 6%,equal to or less than about 5%, equal to or less than about 4%, equal toor less than about 3%, equal to or less than about 2%, equal to or lessthan about 1%, equal to or less than about 0.01%, equal to or less thanabout 0.001%, equal to or less than about 0.0001%, equal to or less thanabout 0.00001%, equal to or less than about 0.000001%, or equal to orless than about 0.0000001%.

In some instances, the non-naturally occurring or modified enzyme (e.g.,non-naturally occurring or modified reverse transcriptase, non-naturallyoccurring or modified non-LTR retrotransposon, non-naturally occurringor modified R2 reverse transcriptase) or a modified polypeptide havingreverse transcriptase activity generates one or more nucleic acid (e.g.,cDNA) molecule(s) complementary to a template at an error rate that isat least about 10000 times lower, at least about 1500 times lower, atleast about 1000 times lower, at least about 500 times lower, at leastabout 100 times lower, at least about 95 times lower, at least about 90times lower, at least about 85 times lower, at least about 80 timeslower, at least about 75 times lower, at least about 70 times lower, atleast about 65 times lower, at least about 60 times lower, at leastabout 55 times lower, at least about 50 times lower, at least about 45times lower, at least about 40 times lower, at least about 35 timeslower, at least about 30 times lower, at least about 25 times lower, atleast about 20 times lower, at least about 15 times lower, at leastabout 10 times lower, at least about 9 times lower, at least about 8times lower, at least about 7 times lower, at least about 6 times lower,at least about 5 times lower, at least about 4 times lower, at leastabout 3 times lower, at least about 2 times lower, or at least about 1time lower than the unmodified or naturally occurring enzyme orunmodified polypeptide having reverse transcriptase activity.

In some instances, the sequencing error rate will be equal to or lessthan about 1 in 100,000 bases. In some instances, the error rate ofnucleotide sequence determination is equal to or less than about 1 in 10bases, 1 in 20 bases, 3 in 100 bases, 1 in 100 bases, 1 in 1000 bases,and 1 in 10,000 bases.

In some instances, the modified enzyme (e.g., modified reversetranscriptase), modified reverse transcriptase, non-naturally occurringenzyme, modified polypeptide having reverse transcriptase activitycomprises at least one modification relative to the wild type,unmodified counterpart, or naturally occurring enzyme. In someinstances, the modified non-LTR retrotransposon comprises at least onemodification of a wild-type or unmodified non-LTR retrotransposon. Insome instances, the modified R2 reverse transcriptase comprises at leastone modification of a wild-type or unmodified R2 reverse transcriptase.In some instances, the modified reverse transcriptase comprises at leastone modification of a wild-type or unmodified reverse transcriptase. Insome instances, the modified polypeptide having reverse transcriptaseactivity comprises at least one modification of a wild-type orunmodified polypeptide having reverse transcriptase activity. In someinstances, the modification comprises at least one truncation (e.g.,N-terminal truncation, C-terminal truncation, and/or N- and C-terminaltruncations). In some instances, the modification comprise(s)site-specific incorporation, and/or addition, and/or deletion, and/orsubstitution of amino acid(s) at positions of interest. In someinstances, the modification enhances the biological properties of themodified enzyme or modified polypeptide relative to the wild-type orunmodified enzyme or polypeptide. In some instances, the modificationimproves at least one enzyme property of the modified enzyme orpolypeptide relative to the wild-type or unmodified enzyme orpolypeptide. In some instances, the modification(s) serve as a point ofattachment for, e.g., labels and protein half-life extension agents, andfor purposes of affixing the variants to the surface of a solid support.In some instances, the present disclosure is related to methods ofproducing cells capable of producing the modified enzymes (e.g.,modified reverse transcriptase) or modified polypeptides, and ofproducing vectors containing DNA or RNA encoding the modified enzymes(e.g., modified reverse transcriptase) or modified polypeptides. In someinstances, the truncation is based on a two-step process. In someinstances, the first step for selecting a truncation includes analyzingthe domains and motifs structure(s) and function(s) of a class ofenzymes, or proteins, or polypeptides. In some instances, the enzymes,or proteins, or polypeptides are non-LTR retrotransposons, reversetranscriptases, R2 reverse transcriptase, LTR retrotransposons, R2non-LTR retrotransposons, or any combination thereof. In some instances,the enzymes, or proteins, or polypeptides are from different organisms.In some instances, all the domains of the enzymes, or proteins, orpolypeptides are present. In some instances, all the domains are presentto ensure reverse transcriptase activity. In some instances, all thedomains are present to ensure the unique properties essential for thepresent disclosure. In some instances, the domains responsible forreverse transcriptase activity are not modified. In some instances, theR2 domain does not comprise modifications. In some instances, the R2domain may comprise modifications. In some instances, the truncatedvariants show expression level. In some instances, the truncatedvariants that show promising expression level are further subject tosmall adjustment(s) in the sequence (step two). In some instances, thesmall adjustment(s) in the sequence include deletion, insertion, and/orsubstitution of amino acid(s). In some instances, the deletion,insertion, and/or substitution of amino acid(s) may include one orseveral amino acid(s). In some instances, the deletion, insertion,and/or substitution of amino acid(s) further optimize expression and/orstability (e.g., thermostability).

In some instances, the modified enzyme (e.g., modified reversetranscriptase), modified reverse transcriptase, or modified polypeptideshas an N-terminal truncation, a C-terminal truncation, or both, relativeto the wild type or unmodified enzyme (e.g., wild-type reversetranscriptase) or wild-type or unmodified polypeptide. In someinstances, the polymerase comprises an N-terminal truncation, aC-terminal truncation, or both. In some instances, the modified reversetranscriptase comprises N-terminal truncation, C-terminal truncation, ora combination of N-terminal and C-terminal truncation(s). In someinstances, the modified enzyme comprises N-terminal truncation,C-terminal truncation, or a combination of N-terminal and C-terminaltruncation(s). In some instances, the modified polypeptide comprisesN-terminal truncation, C-terminal truncation, or a combination ofN-terminal and C-terminal truncation(s). In some instances, the modifiedreverse transcriptase, modified enzyme, modified polypeptide, modifiednon-LTR retrotransposon, or modified R2 reverse transcriptase comprisesa truncation of less than about 100 amino acid residues. In someinstances, the modified reverse transcriptase, modified enzyme, modifiedpolypeptide, modified non-LTR retrotransposon, or modified R2 reversetranscriptase comprises at least one of: (a) an amino-terminaltruncation of less than about 400 amino acid residues and (b) acarboxyl-terminal truncation of less than about 400 amino acid residues.In some instances, the modified reverse transcriptase, modified enzyme,modified polypeptide, modified non-LTR retrotransposon, or modified R2reverse transcriptase lacks up to: about 1, about 2, about 3, about 4,about 5, about 6, about 7, about 8, about 9, about 10, about 11, about12, about 13, about 14, about 15, about 16, about 17, about 18, about19, about 20, about 21, about 22, about 23, about 24, about 25, about30, about 50, about 75, about 100, about 120, about 150, about 175,about 200, about 220, about 250, about 275, about 280, about 290, about300, about 325, about 350, about 375, about 380, about 390, about 400,or about 450 amino acids from the N-terminus, C-terminus, or both. Insome instances, the modified reverse transcriptase, modified enzyme,modified polypeptide, modified non-LTR retrotransposon, or modified R2reverse transcriptase may alternately or additionally have one or moreinternal deletions of up to: about 1, about 2, about 3, about 4, about5, about 6, about 7, about 8, about 9, about 10, about 11, about 12,about 13, about 14, about 15, about 16, about 17, about 18, about 19,about 20, about 21, about 22, about 23, about 24, or about 25 aminoacids, about 30, about 50, about 75, about 100, about 120, about 150,about 175, about 200, about 220, about 250, about 275, about 280, about290, about 300, about 325, about 350, about 375, about 380, about 390,or a total of about 450 amino acids. In some instances, the N-terminaltruncation, C-terminal truncation, or both, may comprise deletions fromabout 1 to about 50 amino acids, from about 1 to about 25, from about 1to about 70, from about 10 to about 50, from about 20 to about 30, fromabout 15 to about 100, from about 1 to about 150, from about 15 to about60, from about 15 to about 40, from about 1 to about 10, from about 10to 35, from about 50 to about 100, from about 20 to about 150, fromabout 200 to about 350, from about 25 to about 350, from about 150 toabout 400, from about 50 to about 400, from about 50 to about 450, fromabout 200 to about 400, or from about 50 to about 350, or from about 50to about 400 amino acids. In some instances, the N-terminal truncationremoves at least about 5, at least about 10, at least about 15, at leastabout 20, at least about 25, at least about 30, at least about 35, atleast about 40, at least about 50, at least about 60, at least about 65,at least about 70, at least about 75, at least about 80, at least about90, at least about 95, at least about 100, at least about 120, at leastabout 130, at least about 140, at least about 150, at least about 175,at least about 200, at least about 220, at least about 250, at leastabout 275, at least about 300, at least about 325, at least about 350,at least about 375, or at least about 400 amino acids. In someinstances, the C-terminal truncation removes at least about 5, at leastabout 10, at least about 15, at least about 20, at least about 25, atleast about 30, at least about 35, at least about 40, at least about 50,at least about 60, at least about 65, at least about 70, at least about75, at least about 80, at least about 90, at least about 95, at leastabout 100, at least about 120, at least about 130, at least about 140,at least about 150, at least about 175, at least about 200, at leastabout 220, at least about 250, at least about 275, at least about 300,at least about 325, at least about 350, at least about 375, or at leastabout 400 amino acids. In some instances, the N-terminal truncationlacks about 5, about 10, about 15, about 20, about 25, about 30, about35, about 40, about 50, about 60, about 65, about 70, about 75, about80, about 90, about 95, about 100, about 120, about 130, about 140,about 150, about 175, about 200, about 220, about 250, about 275, about300, about 325, about 350, about 375, or about 400 amino acids. In someinstances, the C-terminal truncation lacks about 5, about 10, about 15,about 20, about 25, about 30, about 35, about 40, about 50, about 60,about 65, about 70, about 75, about 80, about 90, about 95, about 100,about 120, about 130, about 140, about 150, about 175, about 200, about220, about 250, about 275, about 300, about 325, about 350, about 375,or about 400 amino acids. In some instances, the N-terminal truncationlacks no more than about 5, no more than about 10, no more than about15, no more than about 20, no more than about 25, no more than about 30,no more than about 35, no more than about 40, no more than about 50, nomore than about 60, no more than about 65, no more than about 70, nomore than about 75, no more than about 80, no more than about 90, nomore than about 95, no more than about 100, no more than about 120, nomore than about 130, no more than about 140, no more than about 150, nomore than about 175, no more than about 200, no more than about 220, nomore than about 250, no more than about 275, no more than about 300, nomore than about 325, no more than about 350, no more than about 375, orno more than about 400 amino acids. In some instances, the C-terminaltruncation lacks no more than about 5, no more than about 10, no morethan about 15, no more than about 20, no more than about 25, no morethan about 30, no more than about 35, no more than about 40, no morethan about 50, no more than about 60, no more than about 65, no morethan about 70, no more than about 75, no more than about 80, no morethan about 90, no more than about 95, no more than about 100, no morethan about 120, no more than about 130, no more than about 140, no morethan about 150, no more than about 175, no more than about 200, no morethan about 220, no more than about 250, no more than about 275, no morethan about 300, no more than about 325, no more than about 350, no morethan about 375, or no more than about 400 amino acids. In someinstances, the truncation comprises an N-terminal truncation thatremoves at least about, at most about, or about 5, 10, 15, 20, 25, 30,40, 50, 75, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375,400, 425, 450, 475, or 500 amino acids. In some instances, thetruncation comprises a C-terminal truncation that removes at leastabout, at most about, or about 5, 10, 15, 20, 25, 30, 40, 50, 75, 100,125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450,475, or 500 amino acids. In some instances, the N-terminal truncation,the C-terminal truncation, or both, may be more than about 500 aminoacids, more than about 1000 amino acids, more than about 1500 aminoacids, more than about 2000 amino acids, more than about 5000 aminoacids, more than about 10000 amino acids, more than about 100000 aminoacids, more than about 1000000 amino acids.

In some instances, truncations of regions which do affect functionalactivity of a protein or enzyme may be engineered. In some instances,truncations of regions which do not affect functional activity of aprotein or enzyme may be engineered. A truncation may comprise atruncation of less than about 5, less than about 10, less than about 15,less than about 20, less than about 25, less than about 30, less thanabout 35, less than about 40, less than about 45, less than about 50,less than about 60, less than about 70, less than about 80, less thanabout 90, less than about 100, less than about 125, less than about 150,less than about 200, less than about 250, less than about 300, less thanabout 350, less than about 400 or more amino acids. A truncation maycomprise a truncation of more than about 5, more than about 10, morethan about 15, more than about 20, more than about 25, more than about30, more than about 35, more than about 40, more than about 45, morethan about 50, more than about 60, more than about 70, more than about80, more than about 90, more than about 100, more than about 125, morethan about 150, more than about 200, more than about 250, more thanabout 300, more than about 350, more than about 400 or more amino acids.A truncation may comprise a truncation of about 5%, about 10%, about15%, about 20%, about 25%, about 30%, about 35%, about 40%, about 45%,about 50%, about 55%, about 60%, about 65%, about 70%, about 75%, about80%, about 85%, about 87%, about 90%, about 92%, about 95% or about 100%of the polypeptide or enzyme.

In some instances, the variant or modified enzyme or modified proteinmay comprise one or more modification(s) at an amino acid position. Insome instances, a variant, a mutant, or modified polypeptides or enzymesof the present disclosure may possess an increased activity, such as anincreased RNA-dependent DNA polymerase activity or a DNA-dependent DNApolymerase activity, compared to the corresponding unmutated orunmodified or wildtype polymerase or as compared to one or morepolymerases (e.g., RNA-dependent DNA polymerase, or a reversetranscriptase). In some instances, a polymerase or a reversetranscriptase having an increase in activity may be a modifiedpolymerase or a modified reverse transcriptase that has at least about a5% increase, at least about a 10% increase, at least about a 25%increase, at least about a 30% increase, at least about a 50% increase,at least about a 100% increase, at least about a 150% increase, at leastabout a 200% increase, at least about a 300% increase, at least about a500% increase, at least about a 1,000% increase, at least about a 2,500%increase or at least about a 5,000% increase as compared to (1) thecorresponding unmutated or wild-type enzyme; or (2) a particularpolymerase (e.g., RNA-dependent DNA polymerase, reverse transcriptase)or a particular reverse transcriptase, or a group of polymerases, or agroup of reverse transcriptases. In some instances, the modifiedpolymerase or the modified reverse transcriptase of the presentdisclosure may have an increase in activity of from about 5% to about5,000%, from about 5% to about 2,500%, from about 5% to about 1000%,from about 5% to about 500%, from about 5% to about 250%, from about 5%to about 100%, from about 5% to about 50%, from about 5% to about 25%,from about 25% to about 5,000%, from about 25% to about 2,500%, fromabout 25% to about 1,000%, from about 25% to about 500%, from about 25%to about 250%, from about 25% to about 100%, from about 100% to about5,000%, from about 100% to about 2,500%, from about 100% to about 1000%,from about 100% to about 500%, or from about 100% to about 250%. Anincrease in RNA-dependent DNA polymerase activity and/or DNA-dependentDNA polymerase for a modified polymerase or modified reversetranscriptase of the present disclosure may also be measured accordingto relative activity compared to (1) the corresponding unmodified orwild-type enzyme; or (2) a particular polymerase (e.g., RNA-dependentDNA polymerase, reverse transcriptase) or a particular reversetranscriptase, or a group of polymerases, or a group of reversetranscriptases. In some instances, the increase in such relativeactivity is at least about 1.1, 1.2, 1.5, 2, 5, 10, 25, 50, 75, 100,150, 200, 300, 500, 1,000, 2,500, 5,000, 10,000, or 25,000 fold when theactivity of a modified polymerase or modified reverse transcriptase ofthe present disclosure is compared to (1) the corresponding unmutated orwild-type enzyme; or (2) a particular polymerase (e.g., RNA-dependentDNA polymerase, reverse transcriptase) or a particular reversetranscriptase, or a group of polymerases, or a group of reversetranscriptases. Thus a modified polymerase or modified reversetranscriptase of the present disclosure may have an increasedRNA-dependent DNA polymerase and/or an increased DNA-dependent DNApolymerase activity of from about 1.1 fold to about 25,000 fold, fromabout 1.1 fold to about 10,000 fold, from about 1.1 fold to about 5,000fold, from about 1.1 fold to about 2,500 fold, from about 1.1 fold toabout 1,000 fold, from about 1.1 fold to about 500 fold, from about 1.1fold to about 250 fold, from about 1.1 fold to about 50 fold, from about1.1 fold to about 25 fold, from about 1.1 fold to about 10 fold, fromabout 1.1 fold to about 5 fold, from about 5 fold to about 25,000 fold,from about 5 fold to about 5,000 fold, from about 5 fold to about 1,000fold, from about 5 fold to about 500 fold, from about 5 fold to about100 fold, from about 5 fold to about 50 fold, from about 5 fold to about25 fold, from about 50 fold to about 25,000 fold, from about 50 fold toabout 5,000 fold, from about 50 fold to about 1,000 fold, from about 50fold to about 500 fold, from about 50 fold to about 100 fold, from about100 fold to about 25,000 fold, from about 1,000 fold to about 25,000fold, from about 4,000 fold to about 25,000 fold, from about 10,000 foldto about 25,000 fold, from about 15,000 fold to about 25,000 fold, fromabout 1,000 fold to about 10,000 fold, from about 2,500 fold, to about10,000 fold, from about 5,000 fold to about 10,000 fold, from about7,500 fold to about 10,000 fold, from about 1,000 fold to about 15,000fold, from about 2,500 fold, to about 15,000 fold, from about 5,000 foldto about 15,000 fold, from about 7,500 fold to about 15,000 fold, fromabout 10,000 fold to about 15,000 fold, or from about 12,500 fold toabout 15,000 fold.

In some instances, the polypeptides, proteins, enzymes, modified enzymes(e.g., modified reverse transcriptase), modified polypeptides,non-naturally occurring enzymes, or variants comprise a fusion with, butnot limited to, a protein, a domain, a fusion partner, a carrierprotein, a target sequence, an antigenic determinant, or any combinationthereof. In some instances, the reverse transcriptase or modifiedreverse transcriptase is fused to a protein, a domain, a fusion partner,a target sequence, an antigenic determinant, or any combination thereof.In some instances, the non-LTR retrotransposon or modified non-LTRretrotransposon is fused to a protein, a domain, a fusion partner, atarget sequence, an antigenic determinant, or any combination thereof.In some instances, the modified LTR retrotransposon is fused to aprotein, a domain, a fusion partner, a target sequence, an antigenicdeterminant, or any combination thereof. In some instances, the modifiedR2 non-LTR retrotransposon is fused to a protein, a domain, a fusionpartner, a target sequence, an antigenic determinant, or any combinationthereof. In some instances, the modified R2 reverse transcriptase isfused to a protein, a domain, a fusion partner, a target sequence, anantigenic determinant, or any combination thereof. In some instances,the modified reverse transcriptase is fused to a protein, a domain, afusion partner, a target sequence, an antigenic determinant, or anycombination thereof. In some instances, the variant is fused to aprotein, a domain, a fusion partner, a target sequence, an antigenicdeterminant, or any combination thereof. In some instances, thepolypeptide having reverse transcriptase activity is fused to a protein,a domain, a fusion partner, a target sequence, an antigenic determinant,or any combination thereof.

In some instances, the fused polypeptides, proteins, enzymes, modifiedenzymes (e.g., modified reverse transcriptase), modified polypeptides,non-naturally occurring enzymes, or variants thereof increase stability(e.g., increase thermostability), increase shelf life, increase activefraction(s), and/or improve purification compared to the wild-typecounterpart, naturally occurring enzyme, or unfused polypeptides,proteins, enzymes, or variants thereof. In some instances, a modifiedreverse transcriptase comprises a fusion partner or a carrier protein.In some instances, the selection of the fusion protein, domain, fusionpartner, target sequence, antigenic determinant, or any combinationthereof is based on the mechanism causing reduced or increased stability(e.g., increased thermostability), reduced or increased shelf life,and/or reduced or increased expression level (Costa et al., “Fusion tagsfor protein solubility, purification and immunogenicity in Escherichiacoli: the novel Fh8 system. Front Microbiol. 2014 Feb. 19; 5:63). Insome instances, the fusion tags enhance the solubility of their partnerproteins. In some instances, the fusion proteins form micelle-likestructures. In some instances, the micelle-like structures are misfoldedor unfolded proteins that are sequestered and protected from the solventand/or the soluble protein domains face outward. In some instances, thefusion partners attract chaperones. In some instances, the fusion tagdrives its partner protein into a chaperone-mediated folding pathway. Insome instances, the MBP and/or N-utilization substance (NusA) are twofusion tags that present this mechanism. In some instances, the fusionpartners have an intrinsic chaperone-like activity. In some instances,the hydrophobic patches of the fusion tag interact with partially foldedpassenger proteins, preventing self-aggregation, and promoting properfolding. In some instances, the solubility enhancer partners may play apassive role in the folding of their target proteins, reducing thechances for protein aggregation. In some instances, the fusion partnersnet charges. In some instances, the highly acidic fusion partnersinhibit protein aggregation. In some instances, the fusion is with, butit is not limited to, Fh8, MBP, NusA, Trx, SUMO, GST, SET, GB1, ZZ,HaloTag, SNUT, Skp, T7PK, EspA, Mocr, Ecotin, CaBP, ArsC, IF2-domain I,an expressivity tag, an expressivity tag that is part of IF2-domain I,RpoA, SlyD, Tsf, RpoS, PotD, Crr, msyB, yjgD, rpoD, His6, or anycombination thereof. In some instances, the fusion enhances proteinsolubility and/or purification. In some instances, the Fh8 may act as aneffective solubility enhancer partner and/or robust purification. Insome instances, the Fh8 fusion tag has an amino acid sequence comprisingMPSVQEVEKLLHVLDRNGDGKVSAEELKAFADDSKCPLDSNKIKAFIKEHDKNKDGKL DLKELVSILSS(SEQ ID NO: 21). In some instances, the codon optimized sequencecomprises ATGCCGTCTGTTCAGGAAGTTGAAAAACTGCTGCACGTTCTGGACCGTAACGGTGACGGTAAAGTTTCTGCGGAAGAACTGAAAGCGTTCGCGGACGACTCTAAATGCCCGCTGGACTCTAACAAAATCAAAGCGTTCATCAAAGAACACGACAAAAACAAAGACGGTAAACTGGACCTGAAAGAACTGGTTTCTATCCTGTCTTCTTAG (SEQ ID NO: 22). In someinstances, an enzyme, or a modified enzyme (e.g., modified reversetranscriptase), or a protein (e.g., modified protein), or a polypeptide(e.g., modified polypeptide), or a variant, or a product, or a nucleicacid molecule, or a cDNA molecule, or a template, or an acceptor nucleicacid molecule, or a primer, or an RNA, or a DNA, or a fragment nucleicacid, or a degraded nucleic acid, of the present disclosure may compriseone or more tag(s). In some instances, the fragmented or degraded RNA orDNA, or a variant thereof may comprise one or more tag(s). In someinstances, the R2 reverse transcriptase, or a variant thereof, maycomprise one or more tag(s). In some instances, the non-LTRretrotransposon protein or polypeptide having reverse transcriptaseactivity, or a variant thereof, may comprise one or more tag(s). In someinstances, the cDNA molecule may comprise one or more tag(s). In someinstances, the tag may be captured on a solid support, facilitating theisolation of the enzyme, or protein, or polypeptide, or a variant, or aproduct of the present disclosure. In some instances, the tag may bebiotin that can be recognized by avidin. The affinity tag may includemultiple biotin residues for increased binding to multiple avidinmolecules. In some instances, the tag may include a functional groupsuch as an azido group or an acetylene group, which enables capturethrough copper(I) mediated click chemistry (see H. C. Kolb and K. B.Sharpless, Drug Discovery Today, 2003, 8(24), 1128-1137). In someinstances, the tag may include an antigen that may be captured by anantibody bound on a solid support. In some instances, the tag mayinclude, but is not limited to, His-tag, His6-tag, Calmodulin-tag, CBP,CYD (covalent yet dissociable NorpD peptide), Strep II, FLAG-tag,HA-tag, Myc-tag, S-tag, SBP-tag, Softag-1, Softag-3, V5-tag, Xpress-tag,Isopeptag, SpyTag, B, HPC (heavy chain of protein C) peptide tags, GST,MBP, biotin, biotin carboxyl carrier protein,glutathione-S-transferase-tag, green fluorescent protein-tag, maltosebinding protein-tag, Nus-tag, Strep-tag, thioredoxin-tag, andcombinations thereof. In some instances, the tagged molecule may besubjected to sequencing.

In some instances, a molecular barcode may be attached to any region ofa molecule. For example, the molecular barcode may be attached to the 5′or 3′ end of a polynucleotide (e.g., DNA, RNA). For example, thetarget-specific region of the molecular barcode comprises a sequencethat is complementary to a sequence in the 5′ region of the molecule.The target-specific region of the molecular barcode may also comprise asequence that is complementary to a sequence in the 3′ region of themolecule. In some instances, the molecular barcode is attached a regionwithin a gene or gene product. For example, genomic DNA is fragmentedand a sample tag or molecular identifier label is attached to thefragmented DNA. In other instances, an RNA molecule is alternativelyspliced and the molecular barcode is attached to the alternativelyspliced variants. In another example, the polynucleotide is digested andthe molecular barcode is attached to the digested polynucleotide. Inanother example, the target-specific region of the molecular barcodecomprises a sequence that is complementary to a sequence within themolecule.

In some instances the method of the present disclosure comprisesintroducing a biotin moiety or another affinity purification moiety to,for example, a nucleic acid molecule, such as DNA, RNA, or a combinationof DNA and RNA. In some instances, the method further comprisesimmobilizing the affinity purification tagged nucleic acid molecule on asolid support. In some instances the solid support is a sepharose resinor magnetic beads having an affinity purification material, such asavidin, streptavidin, chitin, glutathione and the like, bound thereto.

In some instances, the enzyme, or protein, or polypeptide, or a variant,or a product of the present disclosure may be bound to a solid support.In some instances, the fragmented or degraded nucleic acid (e.g., RNA orDNA), or a variant thereof may be bound to a solid support. In someinstances, the R2 reverse transcriptase, or a variant thereof, may bebound to a solid support. In some instances, the non-LTR retrotransposonprotein or polypeptide having reverse transcriptase activity, or avariant thereof, may be bound to a solid support. In some instances, thecDNA molecule may be bound to a solid support. In some instances, thesolid support may be glass, plastic, porcelain, resin, sepharose,silica, or other material. In some instances, the solid support may be aplate that is substantially flat substrates, gel, microbeads, magneticbeads, membrane, or other suitable shape and size. In some instances,the microbeads may have diameter between 10 nm to several millimeters.In some instances, the solid support may be non-porous or porous withvarious density and size of pores. In some instances the DNA and/or RNAfragment may be captured on a solid support, unwanted DNA and/or RNA maybe washed away. In some instances, the DNA and/or RNA fragment may bereleased from the solid support, for example, by using restrictionenzyme.

In some instances, the solid support may comprise the target nucleicacid binding region, wherein the target nucleic acid binding regioncomprises a sequence selected from the group consisting of agene-specific sequence, an oligo-dT sequence, a random multimer, and anycombination thereof. In some instances, the solid support furthercomprises a target nucleic acid or complement thereof. In someinstances, the solid support comprises a plurality of target nucleicacids or complements thereof comprising from about 0.01% to about 100%of transcripts of a transcriptome of an organism or complements thereof,or from about 0.01% to about 100% of genes of a genome of an organism orcomplements thereof. In some instances, the cellular labels of theplurality of oligonucleotides comprise a first random sequence connectedto a second random sequence by a first label linking sequence; and themolecular labels of the plurality of oligonucleotides comprise randomsequences. In some instances, the solid support is selected from thegroup consisting of a polydimethylsiloxane (PDMS) solid support, apolystyrene solid support, a glass solid support, a polypropylene solidsupport, an agarose solid support, a gelatin solid support, a magneticsolid support, a pluronic solid support, and any combination thereof. Insome instances, the plurality of oligonucleotides comprise a linkercomprising a linker functional group, and the solid support comprises asolid support functional group; wherein the solid support functionalgroup and linker functional group connect to each other. In someinstances, the linker functional group and the solid support functionalgroup are individually selected from the group consisting of C6, biotin,streptavidin, primary amine(s), aldehyde(s), ketone(s), and anycombination thereof. In some instances, molecular labels of theplurality of oligonucleotides comprise at least 15 nucleotides.

In some instances, fusion partners may be removed from their targetprotein by enzymatic cleavage, chemical cleavage, and/or by using an invivo cleavage strategy. In some instances, proteases may be used for tagremoval. In some instances, the protease may be an endoprotease, serineprotease, factor Xa, enterokinase, alpha-thrombin, a viral protease,tobacco etch virus (TEV), the human rhinovirus 3C protease, SUMOprotease, exoprotease, metallocarboxypeptidase, or aminopeptidase. Insome instances, a fusion tag may be removed by two purification steps.In some instances, the initial affinity purification step includes(e.g., via a histidine tag located at the N-terminal of the fusionprotein), the purified fusion protein mixed in solution with theendoprotease (e.g., a his-tagged protease) to cleave off the tag. Thecleaved target protein may be recovered in the flow-through sample aftera second affinity purification step, in which the cleaved fusion tag andthe added protease are collected in the eluted sample.

In some instances, the modified enzyme, modified reverse trancriptase,non-naturally occurring enzyme, or modified polypeptide having reversetranscriptase activity of the present disclosure shows activity, iscapable of template jumping, and/or generate a nucleic acid molecule(e.g., cDNA molecule) without thermal cycling. In some instances, themodified reverse trancriptase, modified enzyme, non-naturally occurringenzyme, or the modified polypeptide having reverse transcriptaseactivity of the present disclosure shows activity, is capable oftemplate jumping, and/or generate a nucleic acid, cDNA molecule at atemperature ranging from about 25° C. to about 42° C., from about 12° C.to about 42° C., from about 8° C. to about 50° C., from about 4° C. toabout 60° C., from about 27° C. to about 35° C., from about 28° C. toabout 33° C., from about 29° C. to about 32° C., from about 30° C. toabout 37° C., from about 26° C. to about 38° C., from about 30° C. toabout 37° C., from about 25° C. to about 32° C., from about 29° C. toabout 31° C., from about 27° C. to about 38° C., from about 29° C. toabout 38° C. In some instances, the non-naturally occurring enzyme,modified reverse trancriptase, modified enzyme, or modified polypeptidehaving reverse transcriptase activity of the present disclosure showsactivity, is capable of template jumping, and/or generate a nucleic acidmolecule (e.g., cDNA molecule) at about 30° C., or at about 35° C., orat about 25° C. In some instances, the modified enzyme, modified reversetrancriptase, non-naturally occurring enzyme, or modified polypeptidehaving reverse transcriptase activity of the present disclosure showsactivity, is capable of template jumping, and/or generate a nucleic acidmolecule (e.g., cDNA molecule) at a temperature equal to less than about38° C., equal to less than about 42° C., equal to less than about 50°C., equal to less than about 60° C., equal to less than about 35° C.,equal to less than about 30° C., equal to less than about 28° C., equalto less than about 25° C., equal to less than about 20° C., equal toless than about 12° C., equal to less than about 8° C., or equal to lessthan about 4° C. In some instances, the modified enzyme, modifiedreverse trancriptase, non-naturally occurring enzyme, or modifiedpolypeptide having reverse transcriptase activity of the presentdisclosure shows activity, is capable of template jumping, and/orgenerate a nucleic acid molecule (e.g., cDNA molecule) at a temperatureequal to less than about 36° C. In some instances, the modified enzyme,modified reverse trancriptase, non-naturally occurring enzyme, ormodified polypeptide having reverse transcriptase activity of thepresent disclosure shows activity, is capable of template jumping,and/or generate a nucleic acid molecule (e.g., cDNA molecule) at roomtemperature. In some instances, the modified enzyme, modified reversetrancriptase, non-naturally occurring enzyme, or modified polypeptidehaving reverse transcriptase activity of the present disclosure showsactivity, is capable of template jumping, and/or generate a nucleic acidmolecule (e.g., cDNA molecule) at a temperature of at about or of atmost about 8° C., at about or of at most about 12° C., at about or of atmost about 20° C., at about or of at most about 25° C., at about or ofat most about 28° C., at about or of at most about 30° C., at about orof at most about 31° C., at about or of at most about 32° C., at aboutor of at most about 33° C., at about or of at most about 34° C., atabout or of at most about 35° C., at about or of at most about 36° C. atabout or of at most about 39° C., at about or of at most about 40° C.,at about or of at most about 41° C., at about or of at most about 42°C., at about or of at most about 50° C., at about or of at most about55° C., at about or of at most about 60° C. In some instances, themodified enzyme, modified reverse trancriptase, non-naturally occurringenzyme, or modified polypeptide having reverse transcriptase activity ofthe present disclosure shows activity, is capable of template jumping,and/or generate a nucleic acid molecule (e.g., cDNA molecule) at atemperature equal to or less than about any temperature between about42° C. to about 80° C., or between about 35° C. to about 80° C., orbetween about 30° C. to about 50° C., or between about 8° C. to about50° C., or between about 12° C. to about 42° C.

In some instances, a modified enzyme, modified reverse trancriptase,modified polypeptide having reverse transcriptase activity, or anon-naturally occurring enzyme of the present disclosure has at leastone altered characteristic relative to an unmodified or naturallyoccurring enzyme. In some instances, the altered characteristic enablesthe modified enzyme, modified reverse trancriptase, non-naturallyoccurring enzyme, or modified polypeptide having reverse transcriptaseactivity to generate a nucleic acid molecule and/or a complementarydeoxyribonucleic acid (cDNA) molecule from a template nucleic acidmolecule without thermal cycling. In some instances, a modified enzyme,modified reverse trancriptase, modified polypeptide having reversetranscriptase activity, or a non-naturally occurring enzyme of thepresent disclosure is capable of generating one or more copies of thenucleic acid molecule or cDNA molecule at an error rate of at most about0.5%, of at most about 1%, of at most about 1.5%, of at most about 2%,of at most about 2.5%, of at most about 3%, of at most about 3.5%, of atmost about 4%, of at most about 4.5%, of at most about 5%, of at mostabout 6%, of at most about 7%, of at most about 8%, of at most about 9%,of at most about 10%, of at most about 15%, of at most about 20%, of atmost about 25%, of at most about 30%, of at most about 40%, of at mostabout 45%, of at most about 50%, of at most about 60%, of at most about65%, of at most about 70%, of at most about 75%, or of at most about80%. In some instances, the modified enzyme, modified reversetrancriptase, modified polypeptide having reverse transcriptaseactivity, or the non-naturally occurring enzyme of the presentdisclosure is a variant of any one of the sequences disclosed herein. Insome instances, the modified enzyme, modified reverse trancriptase,modified polypeptide having reverse transcriptase activity, or thenon-naturally occurring enzyme of the present disclosure is a variant ofany one of the sequences provided in SEQ ID Nos: 1-20. In someinstances, a modified enzyme, modified reverse trancriptase, modifiedpolypeptide having reverse transcriptase activity, or a non-naturallyoccurring enzyme of the present disclosure has at least one alteredcharacteristic that improves enzyme property relative to an unmodifiedor a naturally occurring enzyme. In some instances, the at least onealtered characteristic that improves enzyme property comprises at leastone of increased/improved stability (e.g., increased/improvedthermostability), increased/improved specific activity,increased/improved protein expression, increased/improved purification,increased/improved processivity, increased/improved strand displacement,increased/improved template jumping, improved single strand DNA priming,and increased/improved fidelity.

In one embodiment, the present disclosure relates to a non-naturallyoccurring enzyme that subjects a template nucleic acid molecule toreverse transcription to generate a complementary deoxyribonucleic acid(cDNA) product and amplification of the cDNA product at a processivityof at least about 80%, at least about 85%, at least about 87%, at leastabout 90%, at least about 92%, at least about 95%, at least about 96%,at least about 97%, at least about 98%, at least about 99%, or at leastabout 99.5% per base as measured at about 12° C., about 15° C., about20° C., about 25° C., about 30° C., about 32° C., about 35° C., about40° C.

In some instances, the non-naturally occurring enzyme has a performanceindex greater than about 1.0 for at least one enzyme property. In someinstances, enzyme property is at least one of the group consisting ofimproved stability (e.g., improved thermostability), specific activity,protein expression, purification, processivity, strand displacement,template jumping, increased DNA/RNA affinity, and fidelity.

In one embodiment, the present disclosure relates to a non-naturallyoccurring enzyme that subjects a template nucleic acid molecule toreverse transcription to generate a complementary deoxyribonucleic acid(cDNA) product, a nucleic acid product, and amplification of the cDNAproduct in a time period of about 3 hours or less and/or at aperformance index greater than about 1.0 for at least one enzymeproperty selected from the group consisting of improved stability (e.g.,improved thermostability), specific activity, protein expression,purification, processivity, strand displacement, template jumping,increased DNA/RNA affinity, and fidelity. In some instances, thetemperature is from about 25° C. to about 40° C. (e.g., about 28° C.,about 30° C., about 32° C., about 35° C., or about 37° C.). In someinstances, the temperature is from about 8° C. to about 50° C. (e.g.,about 8° C., about 20° C., about 42° C., about 45° C., or about 50° C.).

In one embodiment, the present disclosure relates to a non-naturallyoccurring enzyme that subjects a template nucleic acid molecule toreverse transcription to generate a complementary deoxyribonucleic acid(cDNA) product and amplification of the cDNA product in a time period of3 hours or less (e.g., 2.5 hours or less, 2 hours or less, 1.5 hours orless, 1 hour or less, or 30 minutes or less) and/or at a processivityfor a given nucleotide substrate that is at least about 5%, at leastabout 10%, at least about 20%, at least about 30%, at least about 40%,at least about 50%, at least about 60%, at least about 70%, at leastabout 80%, at least about 85%, at least about 88%, at least about 90%,at least about 95%, or at least about 98% higher than the processivityof a reference enzyme for the same nucleotide substrate.

In one embodiment, the present disclosure relates to a non-naturallyoccurring enzyme that subjects a template nucleic acid molecule toreverse transcription to generate a nucleic acid product andamplification of the nucleic acid product in a time period of 3 hours orless (e.g., 2.5 hours or less, 2 hours or less, 1.5 hours or less, 1hour or less, or 30 minutes or less) and/or at a processivity for agiven nucleotide substrate that is at least about 5%, at least about10%, at least about 20%, at least about 30%, at least about 40%, atleast about 50%, at least about 60%, at least about 70%, at least about80%, at least about 85%, at least about 88%, at least about 90%, atleast about 95%, or at least about 98% higher than the processivity of areference enzyme for the same nucleotide substrate.

In one embodiment, the present disclosure provides a method ofamplifying a nucleic acid molecule, comprising subjecting the nucleicacid molecule to nucleic acid amplification using a modified reversetranscriptase. In some instances, the reverse transcriptase is capableof amplifying the nucleic acid molecule at processivity of at leastabout 80%, at least about 88%, at least about 90%, at least about 95%,or at least about 98% per base at about 4° C., about 8° C., about 12°C., about 30° C., about 28° C., about 29° C., about 32° C., about 35°C., about 37° C., about 42° C., about 50° C., or higher than about 42°C.

Methods of Preparing RNA Libraries

In some aspects, the disclosure provides a method for preparing acomplementary deoxyribonucleic acid (cDNA) molecule comprising:partitioning a cell and a non-naturally occurring reverse transcriptase,which cell comprises ribonucleic acid (RNA) molecules; releasing saidRNA molecules from said cell in said partition; and in said partition,using said non-naturally occurring reverse transcriptase to synthesize acomplementary deoxyribonucleic acid (cDNA) library from said RNAmolecule, which non-naturally occurring transcriptase synthesizes saidcDNA library at a processivity of 20 nucleotides or longer percontinuous run, whereby processivity is defined as the number ofreaction enzymes generated in one continuous run without dissociation.In some aspects, the processivity of the enzyme is about 15 nucleotides,16 nucleotides, 17 nucleotides, 18 nucleotides, 19 nucleotides, 20nucleotides per second, 21 nucleotides, 22 nucleotides, 23 nucleotides,24 nucleotides, 25 nucleotides, 26 nucleotides, 27 nucleotides, 28nucleotides, 29 nucleotides, 30 nucleotides, or more.

In some aspects, said non-naturally occurring reverse transcriptase hasat least 80% identity to SEQ ID NOs: 1-20. In some aspects saidpartition further comprises: one or more acceptor nucleic acidmolecules; and a non-naturally occurring reverse transcriptase, whereinsaid non-naturally occurring reverse transcriptase has at least 80%identity to SEQ ID NOs: 1-20.

Methods currently used to conduct library preparation for single celland low input methods include various confinement methods, such asemulsion-based techniques, nanofabrication-based techniques,cell-sorting techniques, and serial dilution-based techniques. Librarypreparation for single cell and low input methods includes manychallenges including but not limited to a risk of artifact amplificationdue to an excess of reaction reagents such as oligo adapters and primersrather than the RNA sample in itself. Achieving quality librarypreparation requires high RNA to DNA conversion efficiency and low oligoadapter-adapter products.

In some aspects, the disclosure provides a method for preparing acomplementary deoxyribonucleic acid (cDNA) molecule for single cell orlow RNA sample input, whereby the RNA sample input is from 5 to 50 pg,from 10 to 50 pg, from 15 to 50 pg, from 20 to 50 pg, from 25 to 50 pg,from 30 to 50 pg, from 35 to 50 pg, from 40 to 50 pg, from 45 to 50 pg.

In some aspects, the disclosure provides an enzymatic platform forpreparing a complementary deoxyribonucleic acid (cDNA) molecule forsingle cell or low RNA sample input, which provides the necessary highRNA-sample-library conversion efficiency. In some instances, the methoddisclosed herein provides a relatively simple protocol with a smallnumber of steps, assuring a small amount of sample loss.

In some aspects, the disclosure provides an enzymatic platform forpreparing a complementary deoxyribonucleic acid (cDNA) molecule forsingle cell or low RNA sample input that is not only limited to targetpoly-adenylated ribonucleic acid (RNA) from cells. In some instances,the enzymatic platform disclosed herein captures non-polyadenylated RNA,such as micro RNA (miRNA), non-coding RNA (ncRNA), long intergenicnoncoding RNA (lincRNA), long non-coding RNA (lnRNA). In some instances,the enzymatic platform disclosed herein captures the full transcriptome,and thus, including but not limited to messenger RNA (mRNA), ribosomalRNA (rRNA), transfer RNA (tRNA), microRNA (miRNA), small interfering RNA(siRNA), small nucleolar RNA (snoRNA), piwi-interacting RNA (piRNA),tRNA-derived small RNA (tsRNA), and small rDNA-derived RNA (srRNA).

In one embodiment, the present disclosure relates to a method forpreparing a concatemer of nucleic acid molecules. In some instances, themethod comprises processing ends of a plurality of double-strandednucleic acid molecules. In some instances, the method comprises adding afirst plurality of adaptor molecules to the plurality of double strandednucleic acid molecules. In some instances, the first plurality ofadaptor molecules comprise one or more overhang sequences. In someinstances, at least two of the one or more overhang sequences arecomplementary to each other. In some instances, the method provides afirst plurality of adaptor connected double-stranded nucleic acidmolecules. In some instances, the method comprises adding a polymerizingenzyme (e.g., adding a polymerase enzyme to the first plurality ofadaptor connected double-stranded nucleic acid molecules). In someinstances, adding a polymerase enzyme is in the absence of a primer. Insome instances, the method does not comprise adding a primer. In someinstances, the polymerizing enzyme forms a first set of adaptorconnected double-stranded nucleic acid concatemers. In some instances,forming a first set of adaptor connected double-stranded nucleic acidconcatemers is by joining two or more adaptor connected double-strandednucleic acid molecules by the one or more overhang sequences. In someinstances, the method comprises adding a second plurality of adaptormolecules to the first set (e.g., first adaptor molecules). In someinstances, the second plurality of adaptor molecules comprises one ormore overhang sequences. In some instances, at least two of the one ormore overhang sequences are complementary to each other. In someinstances, the method provides a second set of adaptor connecteddouble-stranded nucleic acid molecules. In some instances, any one ofthe previous instances can be repeated with a set of adaptor moleculesto yield a concatemer comprising a predetermined average length.

In one embodiment, the present disclosure relates to a method forpreparing a concatemer of nucleic acid molecules. In some instances, themethod comprises subjecting at least one nucleic acid molecule and/or aplurality of double-stranded nucleic acid molecules to end-repair. Insome instances, the method comprises adding at least one or a pluralityof adaptor molecules to the at least one nucleic acid molecule and/orthe plurality of double-stranded nucleic acid molecules. In someinstances, adding at least one or a (first) plurality of adaptormolecules to the at least one nucleic acid molecule and/or the pluralityof double stranded nucleic acid molecules comprises ligation. In someinstances, adding at least one or a (first) plurality of adaptormolecules to the at least one nucleic acid molecule and/or the pluralityof double stranded nucleic acid molecules comprises a reversetranscriptase (e.g., R2 reverse transcriptase, or a modified reversetranscriptase). In some instances, In some instances, the at least oneor a plurality of adaptor molecules comprise one or more overhangsequences. In some instances, at least two overhang sequences arecomplementary to each other (e.g., thereby providing a (first) pluralityof adaptor connected double-stranded nucleic acid molecules). In someinstances, the at least one or a plurality of adaptor molecules comprisea sequence (e.g., overhang sequence) that attaches/ligates to the 3′ endof the nucleic acid molecule and/or a sequence (e.g., overhang sequence)that attaches/ligates to the 5′ end of the nucleic acid molecule. Insome instances, the nucleic acid molecule comprises adaptors on both the3′ and the 5′ end. In some instances, the adaptor that binds to the 3′end is complementary to the adaptor that binds to the 5′ end. In someinstances, the sequence of the adaptors is unknown. In some instances,the sequence of the adaptors is pre-determined. In some instances, theadaptor serves as a template and/or as a primer. In some instances, theadaptor that binds to the 3′ end of one nucleic acid molecule can bindto an adaptor on the 5′ end of another nucleic acid molecule. In someinstances, the method further comprises adding a polymerase enzyme tothe adaptor connected to a nucleic acid molecule. In some instances, themethod further comprises adding a polymerase to the (first) plurality ofadaptor connected double-stranded nucleic acid molecules. In someinstances, the polymerase is added in the absence of a primer. In someinstances, the polymerase enzyme forms a first set of adaptor connecteddouble-stranded nucleic acid concatemers by joining two or more adaptorconnected double-stranded nucleic acid molecules by the one or moreoverhang sequences. In some instances, the polymerase permits that theadaptor connected to the nucleic acid molecule form concatemers. In someinstances, the method comprises adding a second plurality of adaptormolecules to the first set. In some instances, the second plurality ofadaptor molecules comprise one or more overhang sequences. In someinstances, the at least two overhang sequences are complementary to eachother. In some instances, a second set of adaptor connecteddouble-stranded nucleic acid molecules is formed. In some instances, theconcatemer length or the number of attached templates can be determined,for example, by tagging the adaptors with modified nucleotides (e.g., byintroducing methylated nucleotides or by inserting dUTP). In someinstances the length of the concatemer can be regulated based on theratio between modified/unmodified adaptors. In some instances theadaptor sequences can serve as a homology priming location (annealed tothe homology spot ssDNA fragments serve as template and primer). In someinstances, the method comprises amplifying the concatemers by PCR orisothermal reaction. In some instances, the reaction in the PCRundergoes a selected number of cycles (the more cycles, the longer theconcatemer) or time (isothermal amplification). In some instances, thereaction is stopped and the (long) dsDNA concatemers are ligated withtwo unique dsDNA adaptors. In some instances, the length of theconcatemer can be manipulated. In some instances, the length of theconcatemer can be determined at least based on the number of PCR cycles,and/or the amount of time (e.g., in an isothermal amplification), and/orbased on the modified nucleotide present in the adaptor. In someinstances, the adaptor comprises a unique molecular identifier sequence(UMI). In some instances, the polymerase enzyme joins two or moreadaptor connected double-stranded nucleic acid molecules in a PCR orisothermal amplification reaction. In some instances, the adaptorcomprises at least one modified nucleotide.

In some instances, the method for preparing a nucleic acid libraryand/or a complementary cDNA library comprises preparing the library inat most about 1 hour, at most about 2 hours, at most about 3 hours, atmost about 4 hours, at most about 5 hours, at most about 7 hours, atmost about 10 hours, at most about 15 hours, or at most about 20 hours.

In one embodiment, the present disclosure relates to methods andprocesses that enable the discovery of novel markers and mutations forcancer, and/or provides approaches for precision medicine. In someinstances, the methods and processes disclosed herein provides forhigher sensitivity to capture minor allele in ctDNA of <0.1% (availablecurrent methods have sensitivity >1%). In some instances, the methodsand/or processes of the present disclosure comprise a 1-pot (e.g.,single vessel), 1-step protocol, and the library is prepared from asample in an amount of time that is equal to or less than about 2 hours.

The present disclosure relates to methods for preparing a complementarydeoxyribonucleic acid (cDNA) molecule. In some instances, the methodcomprises annealing a primer to a template nucleic acid molecule,thereby generating an annealed template nucleic acid molecule. In someinstances, the method further comprises mixing, in the presence ofnucleotides, the annealed template nucleic acid molecule, a one or moreacceptor nucleic acid molecules, and a modified reverse transcriptase.In some instances, the modified reverse transcriptase generates aplurality of continuous complementary deoxyribonucleic acid molecules.In some instances, the plurality of continuous complementarydeoxyribonucleic acid molecules are prepared in at most about 2 hours.In some instances, the plurality of continuous complementarydeoxyribonucleic acid molecules is generated by having the modifiedreverse transcriptase reverse transcribe a sequence of the annealedtemplate nucleic acid molecule. In some instances, the modified reversetranscriptase then migrates to an acceptor nucleic acid molecule (e.g.,one or more acceptor nucleic acid molecules). In some instances, thereverse transcriptase (e.g., modified reverse transcriptase) is able toreverse transcribe a sequence of the template and/or the acceptornucleic acid molecule at a temperature of from about 12° C. to about 42°C. In some instances, the reverse transcriptase (e.g., modified reversetranscriptase) is able to reverse transcribe a sequence of the templateand/or the acceptor nucleic acid molecule at a temperature of from about8° C. to about 50° C. (e.g., about 8° C., about 15° C., about 20° C.,about 25° C., about 30° C., about 35° C., about 40° C., about 45° C.,about 48° C.). In some instances, the reverse transcriptase (e.g.,modified reverse transcriptase) is able to reverse transcribe a sequenceof the template and/or the acceptor nucleic acid molecule at atemperature of at most about 4° C., at most about 8° C., at most about15° C., at most about 20° C., at most about 25° C., at most about 30°C., at most about 35° C., at most about 40° C., at most about 45° C., orat most about 48° C. In some instances, reverse transcription occurs atan error rate of at most about 5%. In some instances, the reversetranscriptase (e.g., modified reverse transcriptase) is capable ofreverse transcribing the template and/or the acceptor nucleic acidmolecule at an error rate of at most about 45%, at most about 40%, atmost about 35%, at most about 30%, at most about 25%, at most about 20%,at most about 15%, at most about 10%, at most about 8%, at most about7%, at most about 6%, at most about 5%, at most about 4%, at most about3%, at most about 2%, or at most about 1%. In some instances, thereverse transcriptase (e.g., modified reverse transcriptase) can migratefrom the template to the acceptor nucleic acid molecule independently ofsequence identity between the template and the acceptor nucleic acidmolecule. In some instances, the method is prepared in a single vessel.In some instances, the template nucleic acid molecule is a fragmentedDNA template, a fragmented RNA template, a non-fragmented DNA template,a non-fragmented RNA template, or a combination thereof. In someinstances, the method further comprises adding a tag to a templatenucleic acid molecule, thereby generating a plurality of taggedcontinuous complementary deoxyribonucleic acid molecules. In someinstances, the method further comprises performing a polymerase chainreaction amplification reaction, thereby forming one or more amplicons.

The present disclosure relates to methods for preparing a complementarydeoxyribonucleic acid (cDNA) molecule using a modified reversetranscriptase. In some instances, the method for preparing a cDNAmolecule is via template jumping. In some instances, the modifiedreverse transcriptase has an improved enzyme property compared to anaturally occurring or unmodified or wild type enzyme (e.g., wild typereverse transcriptase). In some instances, the method for preparing acDNA molecule comprises: (a) annealing a primer to a template; and (b)mixing, in the presence of nucleotides (e.g., dNTPs), the templateannealed to the primer with a modified reverse transcriptase and anacceptor nucleic acid molecule (e.g., acceptor RNA, DNA, or acombination thereof) under conditions sufficient to generate a cDNAmolecule complementary to the template and/or to the acceptor nucleicacid molecule. In some instances, the enzyme (e.g., modified reversetranscriptase) generates a continuous cDNA molecule by migrating fromthe template to the acceptor nucleic acid molecule. In some instances,template jumping is independent of sequence identity between thetemplate and the acceptor nucleic acid molecule. In some instances, step(a) and step (b) are done at the same time. In some instances, step (a)comprises step (b) (e.g., step (a) and step (b) are merged into onestep). In some instances, at least one of step (a) and/or step (b)further comprises addition of a hot start thermostable polymerase. Insome instances, the method of the present disclosure is performed in asingle tube. In some instances, the method of the present disclosurefurther comprises a polymerase chain reaction (PCR) amplificationreaction. In some instances, the PCR amplification reaction is performedin a single tube (e.g., the same one tube from steps (a) and (b)). Insome instances, all the steps of the method of the present disclosureare performed in a single tube.

The present disclosure relates to a method for preparing a concatemer ofnucleic acid molecules for sequencing. In some instances, the methodcomprises ligating a nucleic acid molecule with a first adaptor. In someinstances, the method further comprises amplifying the ligated nucleicacid molecule by performing a nucleic acid amplification reaction toform a concatemer. In some instances, the amplification reaction isperformed in the absence of a primer. In some instances, the methodfurther comprises ligating the concatemer with a second adaptor. In someinstances, the adaptor(s) (first and/or second adaptor) is/are designedto allow recombination or homology based annealing and extension ofmolecules (e.g., nucleic acid molecules, and/or a template, and/or aprimer, and/or an acceptor). In some instances, the nucleic acidamplification reaction is polymerase chain reaction (PCR) or isothermalamplification. In some instances, the first adaptor comprises a uniquemolecular identifier (UMI) sequence. In some instances, the firstadaptor serves as a primer. In some instances, the first adaptorcomprises single stranded nucleic acid. In some instances, the singlestranded nucleic acid comprises single stranded DNA (ssDNA). In someinstances, the second adaptor comprises double stranded nucleic acid. Insome instances, the double stranded nucleic acid comprises doublestranded DNA (dsDNA). In some instances, the first adaptor is differentfrom the second adaptor. In some instances, the first adaptor comprisestwo or more adaptors. In some instances, the second adaptor comprisestwo or more adaptors. In some instances, both ends of the nucleic acidmolecule comprise an adaptor. In some instances, only one end of thenucleic acid molecule comprises an adaptor. In some instances, both the3′ and the 5′ ends of a nucleic acid molecule comprise an adaptor.

The present disclosure relates to methods for preparing a complementarydeoxyribonucleic acid (cDNA) molecule using a modified reversetranscriptase. In some instances, the method for preparing a cDNAmolecule is via template jumping. In some instances, the modifiedreverse transcriptase has an improved enzyme property compared to anaturally occurring or unmodified or wild type enzyme (e.g., wild typereverse transcriptase). In some instances, the method for preparing acDNA molecule comprises mixing, in the presence of nucleotides (e.g.,dNTPs), a primer, a template, a modified reverse transcriptase and anacceptor nucleic acid molecule (e.g., acceptor RNA, DNA, or acombination thereof) under conditions sufficient to generate a cDNAmolecule complementary to the template and/or to the acceptor nucleicacid molecule. In some instances, the method comprises addition of a hotstart thermostable polymerase (e.g., to the mixing step). In someinstances, the method of the present disclosure is performed in a singletube. In some instances, the method of the present disclosure furthercomprises a polymerase chain reaction (PCR) amplification reaction. Insome instances, the PCR amplification reaction is performed in a singletube (e.g., the same one tube as the mixing step). In some instances,all the steps of the method of the present disclosure is performed in asingle tube (single vessel).

In some instances, the method for preparing a cDNA molecule comprises:(a) annealing one or more primer(s) to a template; and (b) mixing, inthe presence of nucleotides (e.g., dNTPs), the template annealed to oneor more primer(s) with a modified reverse transcriptase and an acceptornucleic acid molecule (e.g., acceptor RNA, DNA, or a combinationthereof) under conditions sufficient to generate a cDNA moleculecomplementary to the template and/or to the acceptor nucleic acidmolecule. In some instances, the method for preparing a cDNA molecule isvia template jumping. In some instances, step (a) and step (b) are doneat the same time. In some instances, step (a) comprises step (b) (e.g.,step (a) and step (b) are merged into one step). In some instances, atleast one of step (a) and/or step (b) further comprises addition of ahot start thermostable polymerase. In some instances, the method of thepresent disclosure is performed in a single tube. In some instances, themethod of the present disclosure further comprises a polymerase chainreaction (PCR) amplification reaction. In some instances, the PCRamplification reaction is performed in a single tube (e.g., the same onetube used in or from steps (a) and (b)). In some instances, all thesteps of the method of the present disclosure is performed in a singletube (i.e. one-pot or single pot).

In some instances, the method for preparing a cDNA molecule comprisesmixing, in the presence of nucleotides (e.g., dNTPs), one or moreprimer(s), a template, a modified reverse transcriptase, and an acceptornucleic acid molecule (e.g., acceptor RNA, DNA, or a combinationthereof) under conditions sufficient to generate a cDNA moleculecomplementary to the template and/or to the acceptor nucleic acidmolecule. In some instances, the method for preparing a cDNA molecule isvia template jumping. In some instances, the method comprises additionof a hot start thermostable polymerase (e.g., to the mixing step). Insome instances, the method of the present disclosure is performed in asingle tube. In some instances, the method of the present disclosurefurther comprises a polymerase chain reaction (PCR) amplificationreaction. In some instances, the PCR amplification reaction is performedin a single tube (e.g., the same one tube as the mixing step). In someinstances, all the steps of the method of the present disclosure isperformed in a single tube.

ssDNA Sponges for RNA Depletion

Ribosomal RNAs can make up as much as 80% or more of the total RNA in asample. It is often desirable to separate mRNA from rRNA because rRNAcan adversely affect the quantitative analysis of mRNA. One approach toseparating rRNA from the other RNA biotypes, including mRNA, miRNA,lncrna, and lincRNA is to deplete the rRNA from the sample. One exampleis the hybridization of rRNA molecules using oligonucleotides, forexample, oligonucleotides homologous to the 5.8S rRNA, 17S rRNA, 18SrRNA, or 28S rRNA in the case of eukaryotic rRNAs, or to the 5S rRNA,16S rRNA, or 23S rRNA in the case of bacterial rRNA. Theoligonucleotides are designed such that they can be “captured” and thehybridization product removed from the sample. For example, theoligonucleotides may be immobilized on a surface such as a column or abead. MICROBExpress (Registered Trademark) and MICROBEnrich (RegisteredTrademark) (Ambion, Austin, Tex.) are examples of commercially availablekits for the depletion of rRNA. Methods and compositions for thedepletion or rRNA from a sample are described in U.S. application Ser.No. 10/029,397, which is incorporated by reference. The poly(A) tail atthe 3′ end of most eukaryotic mRNAs can be used to separate thesemolecules away from rRNA and other non-mRNA species that lack thispoly(A) tail.

Rather than removing the rRNA from samples, in some instances, themethod of the present disclosure contemplates blocking the RNA from anypotential amplification or additional reaction. In some instances, thedisclosure provides a method for processing a sample comprisingmessenger ribonucleic acid (mRNA), ribosomal ribonucleic acid (rRNA)molecules, microRNAs (miRNA), long non-coding RNAs (lncRNA), longintergenic noncoding RNAs (lincRNA), and other RNA biotypes, includingcomprising using said mRNA molecules or other RNA biotypes, includingmiRNA, lncRNA, and lincRNA, to synthesize complementary deoxyribonucleicacid (cDNA) molecules in presence of said rRNA molecules blocked fromtranscription, such that less than 30% of said cDNA molecules comprisesequences from said rRNA molecules.

In some aspects, the disclosure provides a method for processing asample comprising messenger ribonucleic acid (mRNA) and ribosomalribonucleic acid (rRNA) molecules; comprising using said mRNA moleculesto synthesize complementary deoxyribonucleic acid (cDNA) molecules inpresence of said rRNA molecules blocked from transcription, such thatless than 30% of said cDNA molecules comprise sequences from said rRNAmolecules.

In some aspects, the disclosure provides a method for processing amixture comprising a messenger ribonucleic acid (mRNA) and a ribosomalribonucleic (rRNA) molecule, comprising: in said mixture, fragmentingsaid ribosomal ribonucleic (rRNA) molecule to yield a plurality of rRNAfragments; bringing one or more single stranded nucleic sequences incontact with said plurality of rRNA fragments, which one or moresingle-stranded nucleic acids sequences have complementarity with atleast a subset of said rRNA fragments, thereby providing one or morerRNA fragment complexes comprising said one or more single-strandednucleic acids sequences hybridized to said at least said subset of saidrRNA fragments; and using a reverse transcriptase to synthesize at leastone complementary deoxyribonucleic acid (cDNA) molecule from said mRNAin presence of said one or more rRNA fragment complexes (FIGS. 5 and 6).

In some aspects, the complementary to rRNA ssDNA (DNA-sponge) has alinear form with blocked 3′ ends. In some instances, the DNA-sponge hasa circular form. In some instances, the DNA-sponge is concatemerized.FIG. 5 illustrates a DNA-sponge with a circular form, whereas FIG. 5Billustrates a rolling-circle amplification (RCA) product. This figureillustrates the function of the DNA-sponge, which is to anneal to rRNAfragments. The annealing of the rRNA fragments to large complementaryssDNA make the 3′-end of the rRNA fragment not available to Poly Apolymerase or to 3′-priming by R2 enzyme. As such, rRNA fragmentswithout available 3′-ends will not be converted to the sequencinglibrary, as illustrated in FIG. 5 .

Direct RNA and ssDNA Sequencing with R2 Enzyme

In some aspects, the disclosure provides a method for sequencing asingle stranded nucleic acid molecule, comprising providing a reactionmixture comprising said single stranded nucleic acid molecule and anon-naturally occurring enzyme, wherein said non-naturally occurringenzyme comprises a finger domain derived from an R2 retrotransposon, aplam domain derived from an R2 retrotransposon, a thumb domain derivedfrom an R2 retrotransposon; and an endonuclease domain derived from anR2 retrotransposon. In some instances, the method disclosed hereincomprises subjecting said reaction mixture to conditions sufficient touse said non-naturally occurring enzyme to incorporate individualnucleotides into a growing strand complementary to said single strandednucleic acid molecule, wherein incorporation of said individualnucleotides into said growing strand yields detectable signals. In someinstances, the method disclosed herein comprises detecting saiddetectable signals, thereby sequencing said single stranded nucleic acidmolecule.

In some aspects, the disclosure provides a method for sequencing asingle stranded nucleic acid molecule, wherein the said single strandednucleic acid molecule is an RNA molecule. In some instances, the methoddisclosed herein is for sequencing a single stranded nucleic acidmolecule, wherein the single stranded nucleic acid molecule is a singlestranded DNA molecule.

In some aspects, the disclosure provides a method for sequencing asingle stranded nucleic acid molecule, wherein said conditionssufficient to directly sequence said single stranded nucleic acidmolecule comprise optic based single-molecule sequencing conditions.

In some aspects, the disclosure provides a method for sequencing asingle stranded nucleic acid molecule, wherein said conditionssufficient to directly sequence said single stranded nucleic acidmolecule comprise microscopy based single-molecule sequencingconditions.

In some aspects, the disclosure provides a method for sequencing asingle stranded nucleic acid molecule, wherein said conditionssufficient to directly sequence said single stranded nucleic acidmolecule comprise nanopore based single-molecule sequencing conditions.

In some aspects, the disclosure provides a method for sequencing asingle stranded nucleic acid molecule, wherein said conditionssufficient to directly sequence said single stranded nucleic acidmolecule comprise field-effect transistors based single-moleculesequencing conditions.

Common single-molecule sequencing techniques are based on long-reads,whereby several kb fragments are read in one continuous read. In someaspects, the disclosure provides a method whereby the enzyme disclosedherein is capable of efficient template jumping, whereby a large numberof templates can be sequenced in a single continuous sequencing run.

In Situ RNAseq with Non-Naturally Occurring Enzymes

Unlike in situ RNA-sequencing, conventional RNA-sequencing profiles geneexpression over the whole transcriptome, yet still lacks spatialcontext. In situ RNA sequencing, however, allows genome-wide profilingof gene expression in situ in fixed cells and fixed tissue (FIG. 6 ).

In some aspects, the disclosure provides a method comprising preparing acomplementary deoxyribonucleic acid (cDNA) molecule from one or moreribonucleic acid (RNAs), wherein said one or more ribonucleic acid(RNAs) are derived from an in situ tissue of a subject or from a fixedex vivo tissue of said subject with a non-naturally occurring enzyme,wherein said non-naturally occurring enzyme comprises a palm and fingerdomain derived from an R2 retrotransposon, a palm domain derived from anR2 retrotransposon, a thumb domain derived from an R2 retrotransposon,and an endonuclease domain derived from an R2 retrotransposon; therebygenerating a cDNA molecule from said in situ tissue of said subject orfrom said fixed ex vivo tissue of said subject; and sequencing the saidcDNA molecule generated in with the non-naturally occurring enzymedisclosed herein.

In some aspects, the disclosure provides a method comprising preparing acomplementary deoxyribonucleic acid (cDNA) molecule from one or moreribonucleic acid (RNAs), wherein said one or more ribonucleic acid(RNAs) are derived from an in situ tissue of a subject or from a fixedex vivo tissue of said subject with a non-naturally occurring enzyme,wherein said fixed ex vivo tissue of said subject is fixed informaldehyde.

In some aspects, the disclosure provides a method comprising preparing acomplementary deoxyribonucleic acid (cDNA) molecule from one or moreribonucleic acid (RNAs), wherein said one or more ribonucleic acid(RNAs) are derived from an in situ tissue of a subject or from a fixedex vivo tissue of said subject with a non-naturally occurring enzyme,wherein said fixed ex vivo tissue of said subject is fixed and embeddedin paraffin.

In some aspects, the method disclosed herein consists of cDNA that istagged with a barcode, including but not limited to spatial information(FIG. 6 ). The said cDNA can then be converted to a sequencing library.In some instances, the spatial-specific barcoding technique consists ofusing a glass plate with oligonucleotide primers that are printed in aspatial-specific manner. In some instances, the primer used in themethod disclosed herein is a specifically-barcoded polyToligonucleotide. In some aspects, the method disclosed herein is highlysensitive and can operate with very low sample input. In some aspects,the method disclosed herein has a protocol where a random primer isused. In some instances, the method disclosed herein has a protocolwhere a specific primer is used.

In some instances, a biological sample has been purified. In someinstances, a biological sample has not been purified. In some instances,the nucleic acid of a biological sample has not been extracted when thebiological sample is provided to a tube. For example, the RNA or DNA ina biological sample may not be extracted from the biological sample whenproviding the biological sample to a tube. In some instances, a targetnucleic acid (e.g., a target RNA or target DNA) present in a biologicalsample may not be concentrated prior to providing the biological sampleto a reaction vessel (e.g., a tube). Any suitable biological sample thatcomprises nucleic acid may be obtained from a subject.

In some instances, nucleic acid from a biological sample obtained from asubject is amplified. In some cases, the biological sample is obtaineddirectly from the subject. In some instances, a biological sampleobtained directly from a subject refers to a biological sample that hasbeen further processed after being obtained from the subject. In someinstances, a biological sample obtained directly from a subject refersto a biological sample that has not been further processed after beingobtained from the subject, with the exception of any approach used tocollect the biological sample from the subject for further processing.For example, blood is obtained directly from a subject by accessing thesubject's circulatory system, removing the blood from the subject (e.g.,via a needle), and entering the removed blood into a receptacle. Thereceptacle may comprise reagents (e.g., anti-coagulants) such that theblood sample is useful for further analysis. In another example, a swabmay be used to access epithelial cells on an oropharyngeal surface ofthe subject. After obtaining the biological sample from the subject, theswab containing the biological sample can be contacted with a fluid(e.g., a buffer) to collect the biological fluid from the swab.

The present disclosure relates to methods of detecting, diagnosing,and/or prognosing a disease (e.g., cancer) in a subject comprising: (a)obtaining sequence information of a nucleic acid sample (e.g., acell-free nucleic acid sample) derived from a subject and (b) using thesequence information derived from step (a) to detect circulating tumornucleic acid in the sample. In some instances, obtaining sequenceinformation according to step (a) comprises using one or moreadaptor(s). In some instances, the one or more adaptor(s) comprises amolecular barcode. An adaptor can comprise one or more endmodifications. An adaptor can comprise one 5′ phosphate. An adaptor cancomprise two 5′ phosphates. An adaptor can comprise one 3′ hydroxyl. Anadaptor can comprise two 3′ hydroxyls. An adaptor can lack a 3′hydroxyl.

In some instances, the molecular barcode comprises a randomer sequence.In some instances, the method is capable of detecting cell-free nucleicacid that is less than or equal to about 0.75%, 0.50%, 0.25%, 0.1%,0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%, 0.2%, 0.1%, 0.05%, 0.01%,0.009%, 0.008%, 0.007%, 0.006%, 0.005%, 0.004%, 0.003%, 0.002%, 0.001%,0.0005%, or 0.00001%, 1%, 1.75%, 1.5%, 1.25%, 2%, 3%, 4%, 5%, 6%, 8%,9%, 10%, 11%, 12%, 13%, 14% 15%, 16%, 17%, 18%, 19%, 20%, 22%, 25%, 27%,30%, 32%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%,95%, or 100% of total cell-free nucleic acid. In some instances, themethod is capable of detecting circulating tumor nucleic acid that isless than or equal to about 0.75%, 0.50%, 0.25%, 0.1%, 0.9%, 0.8%, 0.7%,0.6%, 0.5%, 0.4%, 0.3%, 0.2%, 0.1%, 0.05%, 0.01%, 0.009%, 0.008%,0.007%, 0.006%, 0.005%, 0.004%, 0.003%, 0.002%, 0.001%, 0.0005%, or0.00001%, 1%, 1.75%, 1.5%, 1.25%, 2%, 3%, 4%, 5%, 6%, 8%, 9%, 10%, 11%,12%, 13%, 14% 15%, 16%, 17%, 18%, 19%, 20%, 22%, 25%, 27%, 30%, 32%,35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%of total circulating nucleic acid. In some instances, the method iscapable of detecting a percentage of circulating tumor nucleic acid (ctnucleic acid) that is less than or equal to 1.75%, 1.5%, 1.25%, 1%,0.75%, 0.50%, 0.25%, 0.1%, 0.9%, 0.8%, 0.7%, 0.6%, 0.5%, 0.4%, 0.3%,0.2%, 0.1%, 0.05%, 0.01%, 0.009%, 0.008%, 0.007%, 0.006%, 0.005%,0.004%, 0.003%, 0.002%, 0.001%, 0.0005%, or 0.00001% of the totalcell-free nucleic acid. In some instances, the sequence informationcomprises information related to at least about 1, 2, 3, 4, 5, 6, 7, 8,9, 10, 15, 20, 25, 30, 35, 40, 50, 70, 80, 100, 200, or 300 genomicregions. In some instances, the sequence information comprisesinformation related to partially all, mostly all, or all genomesequencing. In some instances, concentrations as low as 50 ng of cfDNAmay provide for full genome sequencing.

In some instances, the method of the present disclosure may be used todetermine the presence of a disease (e.g., cancer) in a subject. In someinstances, determining the presence of cancer in a subject comprisesobtaining a sample from a subject and detecting a nucleic acid molecule(e.g., nucleic acid fragment) in the sample according to any of themethods described herein. In some instances, determining the presence ofa disease (e.g., cancer) in a subject comprises amplifying and/orsequencing the nucleic acid molecule. In some instances, the presence ofa nucleic acid molecule is indicative of cancer. In some instances, thepresence of a nucleic acid molecule is indicative of a prenatalcondition. In some instances, the nucleic acid molecule and/or templatecomprises an unknown sequence. In some instances, the sample is abiological sample. In some instances, the biological sample comprisescirculating tumor DNA. In some instances, the biological samplecomprises a tissue sample.

In some instances, the method of the present disclosure comprisesdetecting an amplicon generated by the amplification primers, whereinthe presence of the amplicon determines whether the modified reversetranscriptase is present in the sample.

In some instances, the method of the present disclosure comprisesproviding a prenatal diagnosis based on the presence or absence of anucleic acid molecule (e.g., cDNA molecule).

Preparations of RNA Libraries for Sequencing

In some aspects, the disclosure provides a method for preparing acomplementary deoxyribonucleic acid (cDNA) molecule comprisingfragmenting a ribonucleic acid (RNA) molecule to yield a plurality ofRNA fragments; removing a 3′-phosphate, a 2′-phosphate, and a cyclic2′3′-phosphate group from one or more of said RNA fragments, therebygenerating one or more dephosphorylated fragmented rRNAs; adding apoly-A tail to said one or more dephosphorylated fragmented RNAs;adding, to said one or more dephosphorylated fragmented RNAs: a primeradapter comprising an oligo-T sequence, a poly-T and another adaptersequence compatible with major sequencing technologies; an acceptoradapter; and a non-naturally occurring R2 enzyme having a processivityof 20 nucleotides or longer.

In some aspects, the disclosure provides a method for preparing acomplementary deoxyribonucleic acid (cDNA) molecule, comprising anon-naturally occurring R2 enzyme, wherein said non-naturally occurringR2 enzyme reverse transcribes a sequence from said one or moredephosphorylated fragmented RNAs in a 3′ to 5′ order, wherein said R2enzyme jumps to a 3′-end of said acceptor adapter upon reaching the 5′end of said one or more dephosphorylated fragmented RNAs.

In some aspects, the method disclosed herein consists ofacceptor-adapter that comprises a nucleotide analogue (FIG. 9 ). In someinstances, the said nucleotide analogue is at the 5′ end of saidacceptor-adapter. In some instances, the said acceptor-adaptor comprisesa 3′-dideoxy nucleotide at the acceptor-adapter 3′-end.

In some aspects, the method disclosed herein comprises a non-naturallyoccurring R2 enzyme, wherein said non-naturally occurring R2 enzymereverse transcribes a sequence from said one or more fragmented RNAs ina 3′ to 5′ order, wherein said R2 enzyme jumps to a 3′-end of saidacceptor adapter upon reaching the 5′ end of said one or more fragmentedRNAs (FIGS. 10, 11, and 12 ).

In some instances, a primer may comprise an adaptor sequence. In someinstances, the 5′ tail sequence of a primer comprises a sequence whichdoes not hybridize to a target (the adaptor sequence). The adaptersequence may be selected such that it is the same in a variety ofprimers which have different 3′ target binding sequences (i.e., a“universal” 5′ tail sequence). The adapter sequence is compatible withmajor sequencing technologies including but not limited to, Illumina,Ion Torrent, PacBio, and Roche 454. This allows a single reporter probesequence to be used for detection of any desired target sequence, whichis an advantage in that synthesis of the reporter probe is more complexdue to the labeling. In some instances, a primer may comprise an RNAprimer. In some instances, a primer may comprise a DNA primer. In someinstances, a primer may comprise an R2 RNA primer. In some instances, aprimer may comprise one or more random primer(s).

The present disclosure relates to methods for preparing a nucleic acidmolecule comprising: mixing, in the presence of nucleotides (e.g.,dNTPs), a fragment or degraded template (e.g., a nucleic acid fragment),a primer, a modified reverse transcriptase, and an acceptor nucleic acidmolecule under conditions sufficient to generate a nucleic acidmolecule. In some instances, the acceptor nucleic acid moleculecomprises a modified nucleotide. In some instances, the primer extensionstops at the modified nucleotide. In some instances, the modifiedreverse transcriptase comprises at least one improved enzyme propertyrelative to a wild type, naturally occurring, or unmodified reversetranscriptase. In some instances, the primer is an RNA primer. In someinstances, the primer is an engineered primer (e.g., engineered RNAprimer). In some instances, the primer has been optimized. In someinstances, the primer is an optimized and/or engineered primer (e.g.,optimized and/or engineered RNA primer). In some instances, the primeris RNA R2 primer. In some instances, the method for preparing a nucleicacid molecule is via template jumping. In some instances, the mixingstep of the method of the present disclosure further comprises additionof a hot start thermostable polymerase. In some instances, the method ofthe present disclosure is performed in a single tube. In some instances,the method of the present disclosure further comprises a polymerasechain reaction (PCR) amplification reaction. In some instances, the PCRamplification reaction is performed in the same single tube. In someinstances, all the steps of the method of the present disclosure isperformed in a single tube.

The present disclosure relates to methods for preparing a nucleic acidmolecule comprising: mixing, in the presence of nucleotides (e.g.,dNTPs), a fragment or degraded template (e.g., a nucleic acid fragment),a donor complex, a modified reverse transcriptase, and an acceptornucleic acid molecule under conditions sufficient to generate a nucleicacid molecule. In some instances, the acceptor nucleic acid moleculecomprises a modified nucleotide. In some instances, the primer extensionstops at the modified nucleotide. In some instances, the modifiedreverse transcriptase comprises at least one improved enzyme propertyrelative to a wild type or naturally occurring or unmodified reversetranscriptase. In some instances, the donor complex comprises a templateand a primer. In some instances, the donor complex is a donor R2complex. In some instances, the donor R2 complex comprises an RNA R2primer. In some instances, the method for preparing a nucleic acidmolecule is via template jumping. In some instances, the mixing step ofthe method of the present disclosure further comprises addition of a hotstart thermostable polymerase. In some instances, the method of thepresent disclosure is performed in a single tube. In some instances, themethod of the present disclosure further comprises a polymerase chainreaction (PCR) amplification reaction. In some instances, the PCRamplification reaction is performed in the same single tube (e.g., thesame single tube used to prepare a nucleic acid molecule). In someinstances, all the steps of the method of the present disclosure isperformed in a single tube.

The present disclosure relates to methods for preparing a complementarydeoxyribonucleic acid (cDNA) library using a modified reversetranscriptase. In some instances, the method for preparing a cDNAlibrary uses template jumping. In some instances, the modified reversetranscriptase has an improved enzyme property compared to a naturallyoccurring or wild type or unmodified enzyme (e.g., wild type reversetranscriptase). In some instances, the method for preparing a cDNAlibrary comprises: (a) annealing a primer or one or more primer(s) to atemplate; and (b) mixing, in the presence of nucleotides (e.g., dNTPs),the template annealed to the primer or the template annealed to one ormore primer(s) with a modified reverse transcriptase and an acceptornucleic acid molecule (e.g., acceptor RNA, DNA, or a combinationthereof) under conditions sufficient to generate a cDNA moleculecomplementary to the template and/or to the acceptor nucleic acidmolecule. In some instances, the method for preparing a cDNA librarycomprises mixing, in the presence of nucleotides (e.g., dNTPs), a primeror one or more primer(s), a template, a modified reverse transcriptase,and an acceptor nucleic acid molecule (e.g., acceptor RNA, DNA, or acombination thereof) under conditions sufficient to generate a cDNAmolecule complementary to the template and/or to the acceptor nucleicacid molecule. In some instances, the enzyme (e.g., modified reversetranscriptase) generates a continuous cDNA molecule by migrating fromthe template to the acceptor nucleic acid molecule. In some instances,template jumping is independent of sequence identity between thetemplate and the acceptor nucleic acid molecule. In some instances themethod further comprises amplifying the cDNA molecule to generate a cDNAlibrary. In some instances, step (a) and step (b) are done at the sametime. In some instances, step (a) comprises step (b) (e.g., step (a) andstep (b) are merged into one step). In some instances, the mixing stepor at least one of step (a) and/or step (b) further comprises additionof a hot start thermostable polymerase. In some instances, the method ofthe present disclosure is performed in a single tube. In some instances,the method of the present disclosure further comprises a polymerasechain reaction (PCR) amplification reaction. In some instances, the PCRamplification reaction is performed in a single tube (e.g., the same onetube used in or from the mixing step, or in or from steps (a) and (b)).In some instances, all the steps of the method of the present disclosureis performed in a single tube.

The present disclosure relates to methods for preparing a cDNA and/orDNA library comprising: mixing, in the presence of nucleotides (e.g.,dNTPs), a fragment or degraded template (e.g., a nucleic acid fragment),a primer, a modified reverse transcriptase, and an acceptor nucleic acidmolecule under conditions sufficient to generate a nucleic acid (e.g.,cDNA and/or DNA) molecule. In some instances, the acceptor nucleic acidmolecule comprises a modified nucleotide. In some instances, the primerextension stops at the modified nucleotide. In some instances, themodified reverse transcriptase comprises at least one improved enzymeproperty relative to a wild type or unmodified reverse transcriptase. Insome instances, the primer is an RNA R2 primer. In some instances, themethod further comprises amplifying the nucleic acid (e.g., cDNA and/orDNA) molecule to generate a cDNA library. In some instances, the methodfor preparing a cDNA and/or DNA and/or nucleic acid molecule is viatemplate jumping.

The present disclosure relates to methods for preparing a cDNA and/orDNA library comprising: mixing, in the presence of nucleotides (e.g.,dNTPs), a fragment or degraded template (e.g., a nucleic acid fragment),a donor complex, a modified reverse transcriptase, and an acceptornucleic acid molecule under conditions sufficient to generate a nucleicacid (e.g., cDNA and/or DNA) molecule. In some instances, the acceptornucleic acid molecule comprises a modified nucleotide. In someinstances, the primer extension stops at the modified nucleotide. Insome instances, the modified reverse transcriptase comprises at leastone improved enzyme property relative to a wild type or unmodifiedreverse transcriptase. In some instances, the donor complex comprises atemplate and a primer. In some instances, the donor complex is a donorR2 complex. In some instances, the donor R2 complex comprises an RNA R2primer. In some instances, the method further comprises amplifying thenucleic acid (e.g., cDNA and/or DNA) molecule to generate a cDNA and/orDNA library. In some instances, the method for preparing a cDNA and/orDNA and/or nucleic acid molecule molecule is via template jumping.

In some instances, the method of the present disclosure may comprise adonor complex. In some instances, the donor complex comprises a templateand a primer. In some instances, the method of the present disclosuremay comprise a template. In some instances, the template is a fragmentedand/or degraded template. In some instances, the template is notfragmented. In some instances, the template is RNA, DNA, or acombination of DNA and RNA. In some instances, the RNA is mRNA. In someinstances, the template is mRNA.

The present disclosure relates to methods for preparing a library forsequencing comprising: (a) obtaining a sample with cell-free nucleicacid from a subject; and (b) adding a modified reverse transcriptaseenzyme, a template (e.g., a nucleic acid template), nucleotides, anacceptor nucleic acid molecule, and one or more primer(s) to the nucleicacid. In some instances, the method further comprises conducting anamplification reaction on the cell-free nucleic acid (cf nucleic acid)derived from the sample to produce a plurality of amplicons. In someinstances, the amplification reaction comprises 35 or feweramplification cycles. In some instances, the method comprises producinga library for sequencing. In some instances, the library comprises aplurality of amplicons. In some instances, the modified reversetranscriptase is capable of template jumping and/or comprises at leastone improved enzyme property relative to a wild type or unmodifiedreverse transcriptase. In some instances, the nucleic acid is DNA, RNA,or a combination of RNA and DNA.

The present disclosure relates to a method for preparing a complementarydeoxyribonucleic acid (cDNA) molecule using template jumping, comprisingmixing, in a single tube, a primer or one or more primer(s), a messengerRNA (mRNA) template, nucleotides, a modified reverse transcriptase, anacceptor nucleic acid molecule, and a catalytic metal under conditionssufficient to generate a continuous cDNA molecule. In some instances,the continuous cDNA molecule is complementary to the mRNA templateand/or to the acceptor nucleic acid molecule. In some instances, themodified reverse transcriptase comprises at least one improved enzymeproperty relative to a wild type or unmodified reverse transcriptase. Insome instances, a continuous cDNA molecule is produced. In someinstances, the modified reverse transcriptase undergoes migration fromthe template to the acceptor nucleic acid molecule.

The present disclosure relates to a method for preparing a library forsequencing comprising mixing, in a single tube, a cell-free nucleicacid, a modified reverse transcriptase enzyme, a template, nucleotides,an acceptor nucleic acid molecule, a catalytic metal, and one or moreprimer(s), under conditions sufficient to generate a library. In someinstances, the modified reverse transcriptase comprises at least oneimproved enzyme property relative to a wild type or unmodified reversetranscriptase.

In some instances, the nucleic acid molecule comprises an unknownnucleic acid sequence. In some instances, the template comprises anunknown nucleic acid sequence. In some instances, the migration from thetemplate to the acceptor nucleic acid molecule is independent ofsequence identity between the template and the acceptor nucleic acidmolecule. In some instances, the acceptor nucleic acid moleculecomprises a modified nucleotide that may cause primer extension to stop.In some instances, the cell-free nucleic acid is cell-free DNA (cfDNA),circulating tumor DNA (ctDNA), and/or formalin-fixed, paraffin-embeddedDNA (FFPE DNA), or combinations thereof.

In some instances, a hot start thermostable polymerase may be added to amethod of the present disclosure at or prior to any step of the methodand/or at the same time that a mixing step takes place. For example, ahot start thermostable polymerase may be added at the same time that themodified reverse transcriptase is added to the reaction. The hot startthermostable polymerase may be added at the same time that the acceptornucleic acid molecule is added, and/or at the same time that thetemplate, and/or primer, and/or reverse transcriptase, and/ornucleotides is added to the reaction tube. In some instances, the hotstart thermostable polymerase is added prior to the start of the PCRreaction. In some instances, the hot start thermostable polymerase isadded prior to or at the same time as the RT reaction. In someinstances, the hot start thermostable polymerase is hot start taqpolymerase. Amplification of target nucleic acids can occur on a bead.In some instances, amplification does not occur on a bead. Amplificationcan be by isothermal amplification, e.g., isothermal linearamplification. In some instances, a hot start PCR can be performedwherein the reaction is heated to 95° C. e.g., for two minutes prior toaddition of a polymerase or the polymerase can be kept inactive until afirst heating step in cycle 1. Hot start PCR can be used to minimizenonspecific amplification.

In some instances, the PCR amplification is performed at a temperaturesufficient to inactivate the reverse transcriptase enzyme. In someinstances, the PCR amplification is performed at a temperaturesufficient to activate the hot start thermostable polymerase.

The present disclosure relates to methods of amplifying a cell-freenucleic acid molecule from a sample. In some instances, the sample is abiological sample. In some instances, the cell-free nucleic acidmolecule is subjected to nucleic acid amplification comprising a reversetranscriptase (e.g., modified reverse transcriptase). In some instances,the cell-free nucleic acid molecule is subjected to nucleic acidamplification comprising a reverse transcriptase (e.g., modified reversetranscriptase) under conditions that amplify the nucleic acid moleculeat a specified processivity. In some instances the processivity is of atleast about 80% per base, at least about 81% per base, at least about82% per base, at least about 83% per base, at least about 84% per base,at least about 85% per base, at least about 86% per base, at least about87% per base, at least about 88% per base, at least about 89% per base,at least about 90% per base, at least about 91% per base, at least about92% per base, at least about 93% per base, at least about 94% per base,at least about 95% per base, at least about 96% per base, at least about97% per base, at least about 98% per base, at least about 99% per base,or at least about 100% per base. In some instances, the processivity isperformed at a temperature of about or at most about or at least about12° C., of about or at most about or at least about 13° C., of about orat most about or at least about 14° C., of about or at most about or atleast about 15° C., of about or at most about or at least about 16° C.,of about or at most about or at least about 17° C., of about or at mostabout or at least about 18° C., of about or at most about or at leastabout 19° C., of about or at most about or at least about 20° C., ofabout or at most about or at least about 21° C., of about or at mostabout or at least about 22° C., of about or at most about or at leastabout 23° C., of about or at most about or at least about 24° C., ofabout or at most about or at least about 25° C., of about or at mostabout or at least about 26° C., of about or at most about or at leastabout 27° C. of about or at most about or at least about 28° C., ofabout or at most about or at least about 29° C., of about or at mostabout or at least about 30° C., of about or at most about or at leastabout 31° C., of about or at most about or at least about 32° C., ofabout or at most about or at least about 33° C., of about or at mostabout or at least about 34° C., of about or at most about or at leastabout 35° C., of about or at most about or at least about 36° C., ofabout or at most about or at least about 37° C., of about or at mostabout or at least about 38° C., of about or at most about or at leastabout 39° C., of about or at most about or at least about 40° C., ofabout or at most about or at least about 45° C., of about or at mostabout or at least about 50° C., of about or at most about or at leastabout 60° C., of about or at most about or at least about 70° C., ofabout or at most about or at least about 80° C., of about or at mostabout or at least about 8° C. In some instances the processivity is ofat least about 80% per base, at least about 81% per base, at least about82% per base, at least about 83% per base, at least about 84% per base,at least about 85% per base, at least about 86% per base, at least about87% per base, at least about 88% per base, at least about 89% per base,at least about 90% per base, at least about 91% per base, at least about92% per base, at least about 93% per base, at least about 94% per base,at least about 95% per base, at least about 96% per base, at least about97% per base, at least about 98% per base, at least about 99% per base,or at least about 100% per base, at a temperature of about or at mostabout or of at least about 30° C., or of about or at most about or of atleast about 12° C., of about or at most about or of at least about 45°C., of about or at most about or of at least about 35° C. In someinstances, the reverse transcriptase is a non-LTR retrotransposon or amodified non-LTR retrotransposon. In some instances, the reversetranscriptase is an R2 reverse transcriptase or a modified R2 reversetranscriptase. In some instances, the reverse transcriptase is an R2non-LTR retrotransposon or a modified R2 non-LTR retrotransposon.

The present disclosure relates to methods for preparing a complementarydeoxyribonucleic acid (cDNA) library and/or a DNA library from aplurality of single cells. In some instances, the method comprises thesteps of: releasing nucleic acid from each single cell to provide aplurality of individual nucleic acid samples. In some instances, thenucleic acid in each individual nucleic acid sample is from a singlecell. In some instances, the method further comprises annealing thenucleic acid template to one or more primer(s). In some instances, themethod further comprises mixing the nucleic acid template annealed toone or more primer(s) with an acceptor template (or an acceptor nucleicacid molecule) and a modified reverse transcriptase, in the presence ofnucleotides, under conditions effective for producing a cDNA and/or aDNA molecule. In some instances, the modified reverse transcriptase iscapable of template jumping and/or comprises at least one improvedenzyme property relative to a wild type or unmodified reversetranscriptase. In some instances, the method further comprisesamplifying the cDNA molecule and/or DNA molecule to generate a cDNAand/or DNA library.

The present disclosure relates to methods of detecting a nucleic acidmolecule. In some instances, the method comprises mixing a samplecomprising a nucleic acid molecule with an acceptor template (or anacceptor nucleic acid molecule), a modified reverse transcriptase, aprimer, and nucleotides, under conditions effective for generating anucleic acid molecule. In some instances, the modified reversetranscriptase comprises at least one improved enzyme property relativeto a wild type or unmodified reverse transcriptase. In some instances,the acceptor template (or an acceptor nucleic acid molecule) comprisesat least one modified nucleotide. In some, the modified nucleotide maycause primer extension to stop. In some instances, the method furthercomprises amplifying the nucleic acid molecule.

The present disclosure relates to any method disclosed herein whereinthe methods may further comprise detecting at least one amplicongenerated by the amplification primers. In some instances, the presenceof at least one amplicon indicates the presence of at least one modifiedreverse transcriptase in a sample.

In some instances, any of the methods of the present disclosure does notcomprise a purification step. In some instances, any of the methods ofthe present disclosure comprises at least one purification step. In someinstances, any of the methods of the present disclosure comprises atleast two purification steps. In some instances, any of the methods ofthe present disclosure comprises at least three, at least four, at leastfive, at least six, at least seven, at least eight, at least nine, atleast ten, at least fifteen, or at least twenty purification steps.

The present disclosure relates to a method for preparing a library forsequencing.

In some instances, the modified reverse transcriptase is a modifiednon-retroviral reverse transcriptase. In some instances, the modifiedreverse transcriptase is a modified non-LTR retrotransposon. In someinstances, the modified reverse transcriptase is a modified R2 reversetranscriptase.

In some instances, the sample is a biological sample. In some instances,the biological sample comprises a circulating tumor DNA. In someinstances, the biological sample comprises a tissue sample. In someinstances, the nucleic acid is from a sample. In some instances, thesample is a liquid biopsy sample. In some instances, a sample may be anRNA sample. In some instances, an RNA sample may be used for variouspurposes, including but not limited to PCR, ligation, transcriptomeanalysis, microarray analysis, northern analysis, and cDNA libraryconstruction. In some instances, the present disclosure is directed tomethods for amplifying cDNA libraries from low quantities of cellsand/or single cells in suitable quantity and quality for transcriptomeanalysis through, for example, sequencing or microarray analysis.

In some instances, the nucleic acid and/or a template is of an unknownsequence. In some instances, the nucleic acid and/or a template is RNA,DNA, or a combination of RNA and DNA. In some instances, the RNA ismRNA. In some instances, the mRNA comprises internal priming. In someinstances, the nucleic acid may be a fragmented nucleic acid and/or adegraded nucleic acid. In some instances, the template may be afragmented template and/or a degraded template. In some instances, thenucleic acid may be a non-fragmented nucleic acid and/or a non-degradednucleic acid. In some instances, the template may be a non-fragmentedtemplate and/or a non-degraded template. In some instances, the nucleicacid and/or template is indicative of a disease. In some instances, thenucleic acid and/or template is indicative of cancer. In some instances,the nucleic acid is equal to or less than about 0.01 micromolar. In someinstances, the nucleic acid is between about 0.1 nM to about 100 nM. Insome instances, the nucleic acid is equal to or less than about 500femtomolar.

In some instances, the RNA is obtained from a source selected from thegroup consisting of single cells, cultured cells, tissues, RNAtranscription-based amplified RNA (such as TTR-amplified RNA or otherDNA-dependent RNA polymerase transcribed RNA), RNA-promoter-driventranscribed RNA, aRNA, aRNA-amplified RNA, single-cell mRNA library,isolated mRNA, RNA contained within cells, and combinations of RNAsources. In some instances, the RNA is prepared from a plurality offixed cells, wherein said fixed cells are protected from RNA degradationand also subjected to permeabilisation for enzyme penetration. In someinstances, the fixed cells are obtained from fixative-treated culturalcells, frozen fresh tissues, fixative-treated fresh tissues orparaffin-embedded tissues on slides.

In some instances, the RNA molecule can be the product of in vitrosynthesis or can have been isolated from cells or tissues (Ausubel, et.al., Short Protocols in Molecular Biology, 3rd ed., Wiley, 1995). Cellsand tissues suitable for use in obtaining RNA useful in the practice ofthe present disclosure may include both animal cells and plant cells. Insome instances, the cells include mammalian cells and insect cells. RNAmay also be isolated from prokaryotic cells such as bacteria.

In some instances, the template is RNA, DNA, or a combination of RNA andDNA. In some instances, the template may be a fragmented template and/ora degraded template. In some instances, the template is not degradedand/or fragmented. In some instances, the RNA is mRNA. In someinstances, the template is an RNA template. In some instances, thetemplate is a DNA template. In some instances, the template is a DNAand/or RNA template. In some instances, the template is a mixture of DNAand RNA. In some instances, the RNA comprises any type of RNA (e.g., oneor more of rRNA, tRNA, mRNA, lncRNA, lincRNA, miRNA, and/or snRNA). Insome instances the RNA comprises a mixture of at least one type of RNA.In some instances, the DNA can comprise a mixture of, or at least oneof, genomic DNA or nuclear DNA, mitochondrial DNA, Y-line DNA, autosomalDNA, ribosomal DNA, or a combination thereof. In some instances, thetemplate is a polymer of any length. In some instances, the template isfrom about 20 bases to about 100 bases, from about 30 bases to about 500bases, from about 30 bases to about 1000 bases, from about 50 bases toabout 300 bases, about 100 bases to about 600 bases, about 200 bases toabout 800 bases, about 200 bases to about 600 bases, about 100 bases toabout 2000 bases, about 100 bases and about 2500 bases, about 200 basesto about 5000 bases, about 200 bases to about 1000 bases, about 200 toabout 10000 bases. In some instances, the template is at least about 10bases, at least about 20 bases, at least about 30 bases, at least about40 bases, at least about 50 bases, at least about 60 bases, at leastabout 70 bases, at least about 80 bases, at least about 90 bases, atleast about 100 bases, at least about 150 bases, at least about 200bases, at least about 250 bases, at least about 300 bases, at leastabout 350 bases, at least about 400 bases, at least about 450 bases, atleast about 500 bases, at least about 550 bases, at least about 600bases, at least about 650 bases, at least about 700 bases, at leastabout 750 bases, at least about 800 bases, at least about 850 bases, atleast about 900 bases, at least about 950 bases, at least about 1000bases, at least about 1100 bases, at least about 1200 bases, at leastabout 1300 bases, at least about 1400 bases, at least about 1500 bases,at least about 1700 bases, at least about 2000 bases, at least about2200 bases, at least about 2500 bases, at least about 2700 bases, atleast about 3000, at least about 3500 bases, at least about 4000 bases,at least about 4500 bases, at least about 5000 bases, at least about10,000 bases, or at least about 50,000 bases. In some instances, thetemplate is about or at least about or at most about 10 bases, about orat least about or at most about 20 bases, about or at least about or atmost about 30 bases, about or at least about or at most about 40 bases,about or at least about or at most about 50 bases, about or at leastabout or at most about 60 bases, about or at least about or at mostabout 70 bases, about or at least about or at most about 80 bases, aboutor at least about or at most about 90 bases, about or at least about orat most about 100 bases, about or at least about or at most about 150bases, about or at least about or at most about 200 bases, about or atleast about or at most about 250 bases, about or at least about or atmost about 300 bases, about or at least about or at most about 350bases, about or at least about or at most about 400 bases, about or atleast about or at most about 450 bases, about or at least about or atmost about 500 bases, about or at least about or at most about 550bases, about or at least about or at most about 600 bases, about or atleast about or at most about 650 bases, about or at least about or atmost about 700 bases, about or at least about or at most about 750bases, about or at least about or at most about 800 bases, about or atleast about or at most about 850 bases, about or at least about or atmost about 900 bases, about or at least about or at most about 950bases, about or at least about or at most about 1000 bases, about or atleast about or at most about 1100 bases, about or at least about or atmost about 1200 bases, about or at least about or at most about 1300bases, about or at least about or at most about 1400 bases, about or atleast about or at most about 1500 bases, about or at least about or atmost about 1700 bases, about or at least about or at most about 2000bases, about or at least about or at most about 2200 bases, about or atleast about or at most about 2500 bases, about or at least about or atmost about 2700 bases, about or at least about or at most about 3000,about or at least about or at most about 3500 bases, about or at leastabout or at most about 4000 bases, about or at least about or at mostabout 4500 bases, about or at least about or at most about 5000 bases,about or at least about or at most about 10,000 bases, or about or atleast about or at most about 50,000 bases. In some instances, thetemplate DNA may be a double-stranded DNA template (dsDNA template) or asingle-stranded DNA template (ssDNA template). In some instances, thetemplate RNA may be a double-stranded RNA template (dsRNA template) or asingle-stranded RNA template (ssRNA template).

In some instances, the template is from a single cell. In someinstances, the template is from a plurality of cells. In some instances,the template comprises low copy number DNA, or RNA, or a combination ofDNA and/or RNA. In some instances, low copy number refers to samplesthat contain equal to or less than about 250 picograms (e.g. 100picograms) of for example the template and/or DNA and/or RNA and/or amixture of DNA and RNA. In some instances, the RNA can comprise at leastone of messenger RNA (mRNA), transfer RNA, transfer-messenger RNA,ribosomal RNA, antisense RNA, small nuclear RNA (snRNA), small nucleolarRNA (snoRNA), micro-RNA (miRNA), small interfering RNA (siRNA), longnon-coding RNA (lncRNA), long intervening noncoding (lincRNA), or anycombination thereof. In some instances, the template is from a sample.In some instances, the total amount of template is the total amount oftemplate in a sample. In some instances, the total amount of template isthe total amount of template in a reaction mixture. In some instances,the total amount of template is the total amount of template in one pot(e.g., single vessel). In some instances, the total amount of thetemplate is from about 1 femtomolar (fM) to about 100 micromolar, fromabout 40 femtomolar to about 0.01 micromolar, from about 50 femtomolarto about 500 femtomolar, from about 50 femtomolar to about 0.01micromolar, from about 50 femtomolar to about 0.1 micromolar, from about50 femtomolar to about 500 picomolar, from about 50 femtomolar to about500 nanomolar, from about 50 femtomolar to about 500 micromolar, fromabout 50 femtomolar to about 1 picomolar, from about 40 femtomolar toabout 1 nanomolar, from about 1 femtomolar to about 1 picolomar, fromabout 0.0001 micromolar to about 0.01 micromolar, from about 0.0001micromolar to about 0.1 micromolar, or from about 0.1 nM to about 100nM. In some instances, the total about of template is equal to or atleast about or lower than about 1000 micromolar, equal to or at leastabout or lower than about 500 micromolar, equal to or at least about orlower than about 250 micromolar, equal to or at least about or lowerthan about 100 micromolar, equal to or at least about or lower thanabout 50 micromolar, equal to or at least about or lower than about 25micromolar, equal to or at least about or lower than about 10micromolar, equal to or at least about or lower than about 1 micromolar,equal to or at least about or lower than about 0.1 micromolar, equal toor at least about or lower than about 0.01 micromolar, equal to or atleast about or lower than about 0.001 micromolar, equal to or at leastabout or lower than about 0.0001 micromolar, equal to or at least aboutor lower than about 2000 nanomolar, equal to or at least about or lowerthan about 500 nanomolar, equal to or at least about or lower than about250 nanomolar, equal to or at least about or lower than about 200nanomolar, equal to or at least about or lower than about 50 nanomolar,equal to or at least about or lower than about 25 nanomolar, equal to orat least about or lower than about 20 nanomolar, equal to or at leastabout or lower than about 2 nanomolar, equal to or at least about orlower than about 0.2 nanomolar, equal to or at least about or lower thanabout 0.01 nanomolar, equal to or at least about or lower than about0.001 nanomolar, equal to or at least about or lower than about 0.0001nanomolar, equal to or at least about or lower than about 3000picomolar, equal to or at least about or lower than about 500 picomolar,equal to or at least about or lower than about 250 picomolar, equal toor at least about or lower than about 300 picomolar, equal to or atleast about or lower than about 50 picomolar, equal to or at least aboutor lower than about 25 picomolar, equal to or at least about or lowerthan about 30 picomolar, equal to or at least about or lower than about3 picomolar, equal to or at least about or lower than about 0.3picomolar, equal to or at least about or lower than about 0.01picomolar, equal to or at least about or lower than about 0.001picomolar, equal to or at least about or lower than about 0.0001picomolar, equal to or at least about or lower than about 5000femtomolar, equal to or at least about or lower than about 500femtomolar, equal to or at least about or lower than about 250femtomolar, equal to or at least about or lower than about 50femtomolar, equal to or at least about or lower than about 25femtomolar, equal to or at least about or lower than about 10femtomolar, equal to or at least about or lower than about 1 femtomolar,equal to or at least about or lower than about 0.1 femtomolar, equal toor at least about or lower than about 0.01 femtomolar, equal to or atleast about or lower than about 0.001 femtomolar, equal to or at leastabout or lower than about 0.0001 femtomolar.

In some instances, the template may be present in any nucleic acidsample of interest, including but not limited to, a nucleic acid sampleisolated from a single cell, a plurality of cells (e.g., culturedcells), a tissue, an organ, or an organism (e.g., bacteria, yeast, orthe like). In some instances, the nucleic acid sample is isolated from acell(s), tissue, organ, and/or the like of a mammal (e.g., a human, arodent (e.g., a mouse), or any other mammal of interest). In someinstances, the nucleic acid sample is isolated from a source other thana mammal, such as bacteria, yeast, insects (e.g., Drosophila),amphibians (e.g., frogs (e.g., Xenopus)), viruses, plants, or any othernon-mammalian nucleic acid sample source.

In some instances, the template is optimized. In some instances, theacceptor template or acceptor nucleic acid molecule comprises at leastone modified nucleotide. In some instances, the acceptor template oracceptor nucleic acid molecule is engineered to improve template jumpingand/or conversion efficiency. In some instances, the acceptor templateor acceptor nucleic acid molecule is optimized at the 3′-end. In someinstances, the optimization prevents secondary structure formationand/or nucleotide composition.

In some instances, the methods disclosed in the present disclosure mayfurther comprise optimization of the template (e.g. donor template). Insome instances, optimization of the template comprises contacting thetemplate (e.g. RNA) with an agent capable of removing the 5′ capstructure of the template (e.g., mRNA). In some instances, the removalof the cap structure is performed under conditions permitting theremoval of the cap structure by the agent. In some instances, themethods disclosed in the present disclosure further includedephosphorylation of for example, the decapped template. In someinstances, the method further includes adding a dephosphorylating agentto the decapped template under conditions permitting dephosphorylation.

In some instances, any method of the present disclosure may furthercomprise optimization of the template. In some instances, optimizationof the template comprises: contacting a sample comprising a templatewith an agent that removes a 5′ cap structure of the template, underconditions permitting the removal of the cap structure by the agent. Insome instances, the optimization of the template may further compriseadding a dephosphorylating agent under conditions permitting thedephosphorylation of the decapped template by the agent. In someinstances, the template (e.g. RNA molecule) is dephosphorylated aftersynthesis or isolation. In some instances, the dephosphorylation isachieved by treatment of the nucleic acid (e.g., RNA) molecule withalkaline phosphatase. In some instances, the isolated donor template,such as RNA or mRNA, is decapped and dephosphorylated after isolation.Methods of decapping nucleic acids (e.g., RNAs) include both enzymaticmethods (such as by using a pyrophosphatase such as tobaccopyrophosphatase) and chemical methods (such as periodate oxidation andbeta elimination). Methods for dephosphorylation of nucleic acid (e.g.,RNA) may use alkaline phosphatase. In some instances, the isolated mRNAis decapped (using tobacco acid pyrophosphatase, for example) anddephosphorylated (e.g., by using alkaline phosphatase). In someinstances, the removal of the RNA cap structure is by either enzymatictreatment of the mRNA with a pyrophosphatase or chemical decapping(e.g., by periodate oxidation and beta elimination). In some instances,the mRNA is modified with a tag.

In some instances, template jumping is dependent on the concentration ofthe acceptor nucleic acid molecule.

In some instances, the method of the present disclosure furthercomprises using the modified reverse transcriptase to subject a templatenucleic acid molecule to reverse transcription to yield the nucleic acidmolecule. In some instances, the nucleic acid molecule is a cell-freenucleic acid molecule. In some instances, the template nucleic acidmolecule is a cell-free nucleic acid molecule.

In some instances, primer extension or elongation reactions are utilizedto generate amplified product. Primer extension/elongation reactions maycomprise a cycle of incubating a reaction mixture at a denaturationtemperature for a denaturation duration and incubating a reactionmixture at an elongation temperature for an elongation duration.

Any type of nucleic acid amplification reaction may be used to amplify atarget nucleic acid and generate an amplified product. Moreover,amplification of a nucleic acid may linear, exponential, or acombination thereof. Amplification may be emulsion based or may benon-emulsion based. Non-limiting examples of nucleic acid amplificationmethods include reverse transcription, primer extension, polymerasechain reaction, ligase chain reaction, helicase-dependent amplification,asymmetric amplification, rolling circle amplification, and multipledisplacement amplification (MDA). In some instances, the amplifiedproduct may be DNA. In cases where a target RNA is amplified, DNA can beobtained by reverse transcription of the RNA and subsequentamplification of the DNA can be used to generate an amplified DNAproduct. The amplified DNA product may be indicative of the presence ofthe target RNA in the biological sample. In cases where DNA isamplified, any DNA amplification may be employed. Non-limiting examplesof DNA amplification methods include polymerase chain reaction (PCR),variants of PCR (e.g., real-time PCR, allele-specific PCR, assembly PCR,asymmetric PCR, digital PCR, emulsion PCR, dial-out PCR,helicase-dependent PCR, nested PCR, hot start PCR, inverse PCR,methylation-specific PCR, miniprimer PCR, multiplex PCR, nested PCR,overlap-extension PCR, thermal asymmetric interlaced PCR, touchdownPCR), and ligase chain reaction (LCR). In some cases, DNA amplificationis linear. In some cases, DNA amplification is exponential. In somecases, DNA amplification is achieved with nested PCR, which can improvesensitivity of detecting amplified DNA products.

Denaturation temperatures may vary depending upon, for example, theparticular biological sample analyzed, the particular source of targetnucleic acid (e.g., viral particle, bacteria) in the biological sample,the reagents used, and/or the desired reaction conditions. In someinstances, a denaturation temperature may be from about 80° C. to about110° C. In some instances, a denaturation temperature may be from about90° C. to about 100° C. In some instances, a denaturation temperaturemay be from about 90° C. to about 97° C. In some examples, adenaturation temperature may be from about 92° C. to about 95° C. Instill other examples, a denaturation temperature may be about 80°, 81°C., 82° C., 83° C., 84° C., 85° C., 86° C., 87° C., 88° C., 89° C., 90°C., 91° C., 92° C., 93° C., 94° C., 95° C., 96° C., 97° C., 98° C., 99°C., or 100° C.

Denaturation durations may vary depending upon, for example, theparticular biological sample analyzed, the particular source of targetnucleic acid (e.g., viral particle, bacteria) in the biological sample,the reagents used, and/or the desired reaction conditions. In someinstances, a denaturation duration may be less than or equal to about300 seconds, 240 seconds, 180 seconds, 120 seconds, 90 seconds, 60seconds, 55 seconds, 50 seconds, 45 seconds, 40 seconds, 35 seconds, 30seconds, 25 seconds, 20 seconds, 15 seconds, 10 seconds, 5 seconds, 2seconds, or 1 second. For example, a denaturation duration may be nomore than about 180 seconds, 120 seconds, 90 seconds, 60 seconds, 55seconds, 50 seconds, 45 seconds, 40 seconds, 35 seconds, 30 seconds, 25seconds, 20 seconds, 15 seconds, 10 seconds, 5 seconds, 2 seconds, or 1second.

Elongation or extension temperatures may vary depending upon, forexample, the particular biological sample analyzed, the particularsource of target nucleic acid (e.g., viral particle, bacteria) in thebiological sample, the reagents used, and/or the desired reactionconditions. In some instances, an elongation temperature may be fromabout 30° C. to about 80° C. In some instances, an elongationtemperature may be from about 35° C. to about 72° C. In some instances,an elongation temperature may be from about 45° C. to about 68° C. Insome instances, an elongation temperature may be from about 35° C. toabout 65° C. In some instances, an elongation temperature may be fromabout 40° C. to about 67° C. In some instances, an elongationtemperature may be from about 50° C. to about 68° C. In some instances,an elongation temperature may be about 0° C., 1° C., 2° C., 3° C., 4°C., 5° C., 6° C., 7° C., 8° C., 9° C., 10° C., 11° C., 12° C., 13° C.,14° C., 15° C., 16° C., 17° C., 18° C., 19° C., 34° C., 33° C., 32° C.,31° C., 30° C., 20° C., 21° C., 22° C., 23° C., 24° C., 25° C., 26° C.,27° C., 28° C., 29° C., 35° C., 36° C., 37° C., 38° C., 39° C., 40° C.,41° C., 42° C., 43° C., 44° C., 45° C., 46° C., 47° C., 48° C., 49° C.,50° C., 51° C., 52° C., 53° C., 54° C., 55° C., 56° C., 57° C., 58° C.,59° C., 60° C., 61° C., 62° C., 63° C., 64° C., 65° C., 66° C., 67° C.,68° C., 69° C., 70° C., 71° C., 72° C., 73° C., 74° C., 75° C., 76° C.,77° C., 78° C., 79° C., or 80° C.

Elongation durations may vary depending upon, for example, theparticular biological sample analyzed, the particular source of targetnucleic acid (e.g., viral particle, bacteria) in the biological sample,the reagents used, and/or the desired reaction conditions. In someinstances, an elongation duration may be less than or equal to about 360seconds, less than or equal to about 300 seconds, 240 seconds, 180seconds, 120 seconds, 90 seconds, 60 seconds, 55 seconds, 50 seconds, 45seconds, 40 seconds, 35 seconds, 30 seconds, 25 seconds, 20 seconds, 15seconds, 10 seconds, 5 seconds, 2 seconds, or 1 second. In someinstances, an elongation duration may be no more than about 120 seconds,90 seconds, 80 seconds, 70 seconds, 65 seconds, 60 seconds, 55 seconds,50 seconds, 45 seconds, 40 seconds, 35 seconds, 30 seconds, 25 seconds,20 seconds, 15 seconds, 10 seconds, 5 seconds, 2 seconds, or 1 second.

In some instances, multiple cycles of a primer extension reaction can beconducted. Any suitable number of cycles may be conducted. In someinstances, the number of cycles conducted may be less than about 100,90, 80, 70, 60, 50, 40, 30, 20, 10, or 5 cycles. The number of cyclesconducted may depend upon, for example, the number of cycles (e.g.,cycle threshold value (Ct)) necessary to obtain a detectable amplifiedproduct (e.g., a detectable amount of amplified DNA product that isindicative of the presence of a target RNA in a biological sample). Insome instances, the number of cycles necessary to obtain a detectableamplified product (e.g., a detectable amount of DNA product that isindicative of the presence of a target RNA in a biological sample) maybe less than about or about 100 cycles, 75 cycles, 70 cycles, 65 cycles,60 cycles, 55 cycles, 50 cycles, 40 cycles, 35 cycles, 30 cycles, 25cycles, 20 cycles, 15 cycles, 10 cycles, 8 cycles, 7 cycles, 5 cycles,or 4 cycles. Moreover, in some instances, a detectable amount of anamplifiable product (e.g., a detectable amount of DNA product that isindicative of the presence of a target RNA in a biological sample) maybe obtained at a cycle threshold value (Ct) of less than 100, 75, 70,65, 60, 55, 50, 45, 40, 35, 30, 25, 20, 15, 10, 9, 8, 7, 6, 5, 4, 3, 2,1.

In some instances, an amplification step (e.g., primer amplification,template amplification, nucleic acid amplification) comprises a PCRstep. In some instances, each PCR cycle may comprise a denaturing step,an annealing step, and an extension step. In some instances, each PCRcycle may comprise a denaturing step and an extension step. In someinstances, the PCR comprises at least about or about or at most about 1cycle, at least about or about or at most about 4 cycles, at least aboutor about or at most about 5 cycles, at least about or about or at mostabout 10 cycles, at least about or about or at most about 15 cycles, atleast about or about or at most about 20 cycles, at least about or aboutor at most about 25 cycles, at least about or about or at most about 30cycles, at least about or about or at most about 35 cycles, at leastabout or about or at most about 40 cycles, at least about or about or atmost about 45 cycles, at least about or about or at most about 50cycles, at least about or about or at most about 55 cycles, at leastabout or about or at most about 60 cycles, at least about or about or atmost about 65 cycles, at least about or about or at most about 70cycles, at least about or about or at most about 75 cycles, at leastabout or about or at most about 80 cycles, at least about or about or atmost about 90 cycles, at least about or about or at most about 95cycles, at least about or about or at most about 100 cycles, at leastabout or about or at most about 110 cycles, at least about or about orat most about 120 cycles, at least about or about or at most about 130cycles, at least about or about or at most about 140 cycles, at leastabout or about or at most about 150 cycles, at least about or about orat most about 160. In some instances, the PCR comprises from about 10cycles to 40 cycles, from about 20 cycles to 40 cycles, from about 20cycles to 38 cycles, from about 20 cycles to 35 cycles, from about 10cycles to 35 cycles, from about 10 cycles to 30 cycles, from about 25cycles to 30 cycles, from about 20 cycles to 30 cycles, from about 4cycles to 8 cycles, or from about 28 cycles to 32 cycles. In someinstances, the reaction is heated to 95° C. for 3 minutes before the PCRcycle begins. In some instances, each PCR cycle comprises 95° C. for 3seconds and 62° C. for 20 seconds. In some instances, each PCR cyclecomprises 95° C. for 3 seconds, 54° C. for 10 seconds, and 64° C. for 20seconds. In some instances, each PCR cycle comprises 95° C. for 3seconds and 64° C. for 20 seconds. In some instances, each PCR cyclecomprises 95° C. for 3 seconds and 62° C. for 60 seconds. In someinstances, each PCR cycle comprises 95° C. for 3 seconds, 54° C. for 10seconds, and 64° C. for 10 seconds. In some instances, the PCR comprises30 cycles. In some instances, the reaction is heated to 68° C. after thecompletion of the PCR cycles. In some instances, the reaction is heatedto 68° C. from about 1 second to about 5 seconds, from about 1 second toabout 5 minutes, from about 1 minute to about 5 minutes after thecompletion of the PCR cycles. In some instances, the PCR methodsdescribed herein comprises an extension or elongation step that is atleast about 5 seconds long, at least about 6 seconds long, at leastabout 7 seconds long, at least about 8 seconds long, at least about 9seconds long, at least about 10 seconds long, at least about 11 secondslong, at least about 12 seconds long, at least about 13 seconds long, atleast about 14 seconds long, at least about 15 seconds long, at leastabout 20 seconds long, at least about 30 seconds long, at least about 40seconds long, at least about 50 seconds long, at least about 60 secondslong, at least about 90 seconds long, at least about 120 seconds long,at least about 150 seconds long, at least about 180 seconds long, atleast about 210 seconds long, at least about 240 seconds long, at leastabout 270 seconds long, at least about 300 seconds long, at least about330 seconds long, at least about 360 seconds long, at least about 390seconds long, or more.

The time for which amplification yields a detectable amount of amplifiedproduct indicative of the presence of a target nucleic acid amplifiedcan vary depending upon the biological sample from which the targetnucleic acid was obtained, the particular nucleic acid amplificationreactions to be conducted, and the particular number of cycles ofamplification reaction desired. In some instances, amplification of atarget nucleic acid may yield a detectable amount of amplified productindicative to the presence of the target nucleic acid at time period of120 minutes or less; 90 minutes or less; 60 minutes or less; 50 minutesor less; 45 minutes or less; 40 minutes or less; 35 minutes or less; 30minutes or less; 25 minutes or less; 20 minutes or less; 15 minutes orless; 10 minutes or less; or 5 minutes or less.

In some instances, a biological sample may be preheated prior toconducting a primer extension reaction. The temperature (e.g., apreheating temperature) at which and duration (e.g., a preheatingduration) for which a biological sample is preheated may vary dependingupon, for example, the particular biological sample being analyzed. Insome examples, a biological sample may be preheated for no more thanabout 60 minutes, 50 minutes, 40 minutes, 30 minutes, 25 minutes, 20minutes, 15 minutes, 10 minutes, 9 minutes, 8 minutes, 7 minutes, 6minutes, 5 minutes, 4 minutes, 3 minutes, 2 minutes, 1 minute, 45seconds, 30 seconds, 20 seconds, 15 seconds, 10 seconds, or 5 seconds.In some examples, a biological sample may be preheated at a temperaturefrom about 80° C. to about 110° C. In some examples, a biological samplemay be preheated at a temperature from about 90° C. to about 100° C. Insome examples, a biological sample may be preheated at a temperaturefrom about 90° C. to about 97° C. In some examples, a biological samplemay be preheated at a temperature from about 92° C. to about 95° C. Insome instances, a biological sample may be preheated at a temperature ofabout 80° C., 81° C., 82° C., 83° C., 84° C., 85° C., 86° C., 87° C.,88° C., 89° C., 90° C., 91° C., 92° C., 93° C., 94° C., 95° C., 96° C.,97° C., 98° C., 99° C., or 100° C.

In some instances, reagents necessary for conducting nucleic acidamplification may also include a reporter agent that yields a detectablesignal whose presence or absence is indicative of the presence of anamplified product. The intensity of the detectable signal may beproportional to the amount of amplified product. In some cases, whereamplified product is generated of a different type of nucleic acid thanthe target nucleic acid initially amplified, the intensity of thedetectable signal may be proportional to the amount of target nucleicacid initially amplified. For example, in the case of amplifying atarget RNA via parallel reverse transcription and amplification of theDNA obtained from reverse transcription, reagents necessary for bothreactions may also comprise a reporter agent, may yield a detectablesignal that is indicative of the presence of the amplified DNA product,and/or the target RNA amplified. The intensity of the detectable signalmay be proportional to the amount of the amplified DNA product and/orthe original target RNA amplified. The use of a reporter agent alsoenables real-time amplification methods, including real-time PCR for DNAamplification.

Reporter agents may be linked with nucleic acids, including amplifiedproducts, by covalent or non-covalent linkages or interactions.Non-limiting examples of non-covalent linkates or interactions includeionic interactions, Van der Waals forces, hydrophobic interactions,hydrogen bonding, and combinations thereof. In some instances, reporteragents may bind to initial reactants and changes in reporter agentlevels may be used to detect amplified product. In some instances,reporter agents may only be detectable (or non-detectable) as nucleicacid amplification progresses. In some instances, an optically-activedye (e.g., a fluorescent dye) may be used as may be used as a reporteragent. Non-limiting examples of dyes include SYBR green, SYBR blue,DAPI, propidium iodine, Hoeste, SYBR gold, ethidium bromide, acridines,proflavine, acridine orange, acriflavine, fluorcoumanin, ellipticine,daunomycin, chloroquine, distamycin D, chromomycin, homidium,mithramycin, ruthenium polypyridyls, anthramycin, phenanthridines andacridines, ethidium bromide, propidium iodide, hexidium iodide,dihydroethidium, ethidium homodimer-1 and -2, ethidium monoazide, andACMA, Hoechst 33258, Hoechst 33342, Hoechst 34580, DAPI, acridineorange, 7-AAD, actinomycin D, LDS751, hydroxystilbamidine, SYTOX Blue,SYTOX Green, SYTOX Orange, POPO-1, POPO-3, YOYO-1, YOYO-3, TOTO-1,TOTO-3, JOJO-1, LOLO-1, BOBO-1, BOBO-3, PO-PRO-1, PO-PRO-3, BO-PRO-1,BO-PRO-3, TO-PRO-1, TO-PRO-3, TO-PRO-5, JO-PRO-1, LO-PRO-1, YO-PRO-1,YO-PRO-3, PicoGreen, OliGreen, RiboGreen, SYBR Gold, SYBR Green I, SYBRGreen II, SYBR DX, SYTO-40, -41, -42, -43, -44, -45 (blue), SYTO-13,-16, -24, -21, -23, -12, -11, -20, -22, -15, -14, -25 (green), SYTO-81,-80, -82, -83, -84, -85 (orange), SYTO-64, -17, -59, -61, -62, -60, -63(red), fluorescein, fluorescein isothiocyanate (FITC), tetramethylrhodamine isothiocyanate (TRITC), rhodamine, tetramethyl rhodamine,R-phycoerythrin, Cy-2, Cy-3, Cy-3.5, Cy-5, Cy5.5, Cy-7, Texas Red,Phar-Red, allophycocyanin (APC), Sybr Green I, Sybr Green II, Sybr Gold,CellTracker Green, 7-AAD, ethidium homodimer I, ethidium homodimer II,ethidium homodimer III, ethidium bromide, umbelliferone, eosin, greenfluorescent protein, erythrosin, coumarin, methyl coumarin, pyrene,malachite green, stilbene, lucifer yellow, cascade blue,dichlorotriazinylamine fluorescein, dansyl chloride, fluorescentlanthanide complexes such as those including europium and terbium,carboxy tetrachloro fluorescein, 5 and/or 6-carboxy fluorescein (FAM),5- (or 6-) iodoacetamidofluorescein, 5-{[2 (and3)-5-(Acetylmercapto)-succinyl]amino}fluorescein (SAMSA-fluorescein),lissamine rhodamine B sulfonyl chloride, 5 and/or 6 carboxy rhodamine(ROX), 7-amino-methyl-coumarin, 7-Amino-4-methylcoumarin-3-acetic acid(AMCA), BODIPY fluorophores, 8-methoxypyrene-1,3,6-trisulfonic acidtrisodium salt, 3,6-Disulfonate-4-amino-naphthalimide,phycobiliproteins, AlexaFluor 350, 405, 430, 488, 532, 546, 555, 568,594, 610, 633, 635, 647, 660, 680, 700, 750, and 790 dyes, DyLight 350,405, 488, 550, 594, 633, 650, 680, 755, and 800 dyes, or otherfluorophores.

In some instances, a reporter agent may be a sequence-specificoligonucleotide probe that is optically active when hybridized with anamplified product. Due to sequence-specific binding of the probe to theamplified product, use of oligonucleotide probes can increasespecificity and sensitivity of detection. A probe may be linked to anyof the optically-active reporter agents (e.g., dyes) and may alsoinclude a quencher capable of blocking the optical activity of anassociated dye. Non-limiting examples of probes that may be useful usedas reporter agents include TaqMan probes, TaqMan Tamara probes, TaqManMGB probes, or Lion probes. In some instances, a reporter agent may be aradioactive species. Non-limiting examples of radioactive speciesinclude 14C, 123I, 124I, 125I, 131I, 99mTc, 35S, or 3H. In someinstances, a reporter agent may be an enzyme that is capable ofgenerating a detectable signal. Detectable signal may be produced byactivity of the enzyme with its substrate or a particular substrate inthe case the enzyme has multiple substrates. Non-limiting examples ofenzymes that may be used as reporter agents include alkalinephosphatase, horseradish peroxidase, I2-galactosidase, alkalinephosphatase, β-galactosidase, acetylcholinesterase, and luciferase.

In some instances, an amplified product (e.g., amplified DNA product,amplified RNA product) may be detected. Detection of amplified product,including amplified DNA, may be accomplished with any suitable detectionmethod. The particular type of detection method used may depend, forexample, on the particular amplified product, the type of reactionvessel used for amplification, other reagents in a reaction mixture,whether or not a reporter agent was included in a reaction mixture, andif a reporter agent was used, the particular type of reporter agent use.Non-limiting examples of detection methods include optical detection,spectroscopic detection, electrostatic detection, electrochemicaldetection, and the like. Optical detection methods include, but are notlimited to, fluorimetry and UV-vis light absorbance. Spectroscopicdetection methods include, but are not limited to, mass spectrometry,nuclear magnetic resonance (NMR) spectroscopy, and infraredspectroscopy. Electrostatic detection methods include, but are notlimited to, gel based techniques, such as, for example, gelelectrophoresis, SDS-PAGE gel. Electrochemical detection methodsinclude, but are not limited to, electrochemical detection of amplifiedproduct after high-performance liquid chromatography separation of theamplified products.

In some instances, the time required to complete the elements of amethod may vary depending upon the particular steps of the method. Insome instances, an amount of time for completing the elements of amethod may be from about 5 minutes to about 120 minutes. In someinstances, an amount of time for completing the elements of a method maybe from about 5 minutes to about 60 minutes. In some instances, anamount of time for completing the elements of a method may be from about5 minutes to about 30 minutes. In some instances, an amount of time forcompleting the elements of a method may be less than or equal to 120minutes, less than or equal to 90 minutes, less than or equal to 75minutes, less than or equal to 60 minutes, less than or equal to 45minutes, less than or equal to 40 minutes, less than or equal to 35minutes, less than or equal to 30 minutes, less than or equal to 25minutes, less than or equal to 20 minutes, less than or equal to 15minutes, less than or equal to 10 minutes, or less than or equal to 5minutes.

In some instances, the reaction may have a pH suitable for producing theproduct, for primer extension, protein expression, PCR amplication, ortemplate jumping. In some instances, the pH of the reaction may rangefrom about 5 to about 9, from about 6 to about 9, from about 7 to about9, from about 8 to about 9. In some instances, the pH range is fromabout pH 2 to about pH 10, from about pH 4 to about pH 10, from about pH2 to about pH 8, from about pH 4 to about pH 8, from about pH 5 to aboutpH 8, from about pH 5 to about pH 7, from about pH 6 to about pH 11,from about pH 6 to about pH 12, from about pH 5 to pH 13, from about pH5 to about pH 14. In some instances, the pH is about 2.0, about 2.5,about 3.0, about 3.5, about 4.0, about 4.5, about 5.0, about 5.5, about6.0, about 6.5, about 7.0, about 7.5, about 8.0, about 8.5, about 9.0,about 9.5, about 10.0, about 10.5, about 11, about 11.5, about 12, about12.5, about 13, about 13.5, about 14.

In some instances, any method of the present disclosure may comprise adetergent. In some instances, the detergent is non-ionic and/or azwitterionic detergent. In some instances, a non-ionic detergent isselected from a group consisting of tween, triton, Triton CF-21, TritonCF-32, Triton DF-12, Triton DF-16, Triton GR-SM, Triton N-101(Polyoxyethylene branched nonylphenyl ether), Triton QS-15, TritonQS-44, Triton RW-75 (Polyethylene glycol 260 monoChexadecyl/octadecyl)ether and 1-Octadecanol), Triton X-100 (Polyethylene glycoltert-octylphenyl ether), Triton X-102, Triton X-15, Triton X-151, TritonX-200, Triton X-207, Triton X-114, Triton X-165, Triton X-305, TritonX-405 (polyoxyethylene(40) isooctylphenyl ether), Triton X-405 reduced(polyoxyethylene(40) isooctylcyclohexyl ether), Triton X-45(Polyethylene glycol 4-tert-octylphenyl ether), Triton X-705-70, TWEENin any form including: TWEEN 20 (Polyoxyethylene sorbitan monolaurate),TWEEN 21 (Polyoxyethylene sorbitan monolaurate), TWEEN 40(polyoxyethylene(20) sorbitan monopalmitate), TWEEN 60 (Polyethyleneglycol sorbitan monostearate), TWEEN 61 (Polyethylene glycol sorbitanmonostearate), TWEEN 65 (Polyoxyethylene sorbitan Tristearate), TWEEN 80(Polyoxyethylene sorbitan monooleate), TWEEN 81 (Polyoxyethylenesorbitan monooleate), TWEEN 85 (polyoxyethylene(20) sorbitan trioleate),Brij, Brij 30 (Polyoxyethylene 4 lauryl ether) Brij 35 (Polyoxyethylene23 lauryl ether), Brij 52 (Polyoxyethylene 2 cetyl ether), Brij 56(Polyoxyethylene 10 cetyl ether), Brij 58 (Polyoxyethylene 20 cetylether), Brij 72 (Polyoxyethylene 2 stearyl ether), Brij 76(Polyoxyethylene 10 stearyl ether), Brij 78 (Polyoxyethylene 20 stearylether), Brij 92 (Polyoxyethylene 2 oleyl ether), Brij 97(Polyoxyethylene 10 oleyl ether), Brij 98 (Polyoxyethylene 20 oleylether), Brij 700 (Polyoxyethylene 100 stearyl ether, octylthioglucoside, maltosides, and combinations thereof.

In some instances, any method disclosed herein for producing anymolecule according to the present disclosure comprises at least onesalt. In some instances, the salt is at least one member selected fromthe group consisting of NaCl, LiCl, AlCl₃, CuCl₂, MgCl₂, InCl₃, SnCl₄,CrCl₂, CrCl₃, KCl, NaI, KI, TMACl (tetramethyl ammonium chloride), TEACl(tetraethyl ammonium chloride), KSCN, CsSCN, KCH₃COO, CH₃COONa,C₅H₈KNO₄, C₅H₈NNaO₄, CsCl, and any combination thereof. In someinstances, any method disclosed herein for producing any moleculeaccording to the present disclosure comprises NaCl. In some instances,the conditions sufficient for producing a molecule or a librarycomprises NaCl. In some instances, the reaction may have a saltconcentration and/or NaCl suitable for producing a product, for primerextension, protein expression, PCR amplication, or template jumping. Insome instances, the NaCl concentration is from about 50 mM to about 1000mM, from about 100 mM to about 500 mM, from about 200 mM to about 300mM, from about 200 mM to about 600 mM. In some instances, the NaClconcentration is at least about, at most about, or about 50 mM, at leastabout, at most about, or about 100 mM, at least about, at most about, orabout 150 mM, at least about, at most about, or about 200 mM, at leastabout, at most about, or about 250 mM, at least about, at most about, orabout 300 mM, at least about, at most about, or about 350 mM, at leastabout, at most about, or about 400 mM, at least about, at most about, orabout 450 mM, at least about, at most about, or about 500 mM, at leastabout, at most about, or about 550 mM, at least about, at most about, orat least about, at most about, or about 600 mM, at least about, at mostabout, or about 650 mM, at least about, at most about, or about 700 mM,at least about, at most about, or about 750 mM, at least about, at mostabout, or about 800 mM, at least about, at most about, or about 850 mM,at least about, at most about, or about 900 mM, at least about, at mostabout, or about 950 mM, or at least about, at most about, or about 1000mM. In some instances, the NaCl may improve enzyme activity and/ortemplate jumping of an enzyme or polypeptide of the present disclosure(e.g., of a reverse transcriptase).

In some instances, the reaction may have a nucleotide (e.g. dNTPs)concentration suitable for producing a product, for primer extension,protein expression, PCR amplication, or template jumping. In someinstances, the total dNTP concentration in a reaction may be from about50 μM to about 1000 μM, from about 100 μM to about 500 μM, from about200 μM to about 300 μM, from about 200 μM to about 600 μM. In someinstances, the total dNTP concentration is at least about, at mostabout, or about 50 μM, at least about, at most about, or about 100 μM,at least about, at most about, or about 150 μM, at least about, at mostabout, or about 200 μM, at least about, at most about, or about 250 μM,at least about, at most about, or about 300 μM, at least about, at mostabout, or about 350 μM, at least about, at most about, or about 400 μM,at least about, at most about, or about 450 μM, at least about, at mostabout, or about 500 μM, at least about, at most about, or about 550 μM,at least about, at most about, or at least about, at most about, orabout 600 μM, at least about, at most about, or about 650 PM, at leastabout, at most about, or about 700 μM, at least about, at most about, orabout 750 PM, at least about, at most about, or about 800 μM, at leastabout, at most about, or about 850 PM, at least about, at most about, orabout 900 μM, at least about, at most about, or about 950 PM, or atleast about, at most about, or about 1000 μM. In some instances, thetotal concentration of each dNTP is at least about, at most about, orabout 1 μM; at least about, at most about, or about 2 μM; at leastabout, at most about, or about 3 μM; at least about, at most about, orabout 4 μM; at least about, at most about, or about 5 μM; at leastabout, at most about, or about 6 μM; at least about, at most about, orabout 7 μM; at least about, at most about, or about 8 μM; at leastabout, at most about, or about 9 μM; at least about, at most about, orabout 10 PM; at least about, at most about, or about 15 μM; at leastabout, at most about, or about 20 μM; at least about, at most about, orabout 25 M; at least about, at most about, or about 30 μM; at leastabout, at most about, or about 35 μM; at least about, at most about, orabout 40 μM; at least about, at most about, or about 45 μM; at leastabout, at most about, or about 50 μM; at least about, at most about, orabout 55 μM; at least about, at most about, or about 60 μM; at leastabout, at most about, or about 65 μM; at least about, at most about, orabout 70 μM; at least about, at most about, or about 75 μM; at leastabout, at most about, or about 80 μM; at least about, at most about, orabout 85 μM; at least about, at most about, or about 90 μM; at leastabout, at most about, or about 95 μM; at least about, at most about, orabout 100 μM; at least about, at most about, or about 250 μM; at leastabout, at most about, or about 500 μM; at least about, at most about, orabout 1000 μM; at least about, at most about, or about 10000 μM. In someinstances, the total concentration of each dNTP is from about 2 μM toabout 5 μM, from about 2 μM to about 10 μM, from about 2 μM to about 20μM, from about 2 μM to about 50 μM, from about 2 μM to about 100 μM,from about 2 μM to about 250 μM, from about 5 μM to about 10 μM, fromabout 5 μM to about 50 μM, from about 5 μM to about 250 μM, from about 5μM to about 1000 μM.

In some instances, the concentration of each dNTP may be independent anddifferent from the concentration of one or more dNTP. In some instances,the concentration of each dNTP for example the concentration of eachdCTP, dGTP, dTTP, or dATP may be independent and different from theconcentration of at least one other dNTP. In some instances, theconcentration of one dNTP (e.g., dCTP, dGTP, dTTP, or dATP) may be atleast about or at most about or about 1 fold, 2 fold, 3 fold, 4 fold, 5fold, 7 fold, 10 fold, 20 fold, 35 fold, 50 fold, 75 fold, 90 fold, 100fold, 200 fold, 500 fold, or 1000 fold different from at least one otherdNTP (e.g., dCTP, dGTP, dTTP, or dATP).

In some instances, the reaction mixture includes a pH adjusting agent.pH adjusting agents of interest include, but are not limited to, sodiumhydroxide, hydrochloric acid, phosphoric acid buffer solution, trisbuffer, citric acid buffer solution, and the like. For example, the pHof the reaction mixture can be adjusted to the desired range by addingan appropriate amount of the pH adjusting agent.

The temperature range suitable for production of a product may varyaccording to factors such as the particular polymerase employed, themelting temperatures of any optional primers employed, etc. In someinstances, the polymerase may include, but it is not limited to, areverse transcriptase, a Moloney Murine Leukemia Virus (MMLV) reversetranscriptase, an R2 reverse transcriptase, an RNA-directed DNApolymerase, an DNA-directed DNA polymerase, a non-LTR retrotransposon,an R2 non-LTR retrotransposon, a polypeptide having reversetranscriptase activity, or any variant thereof, or any combinationthereof.

In some instances, the conditions sufficient to produce a productinclude bringing the reaction mixture to a temperature ranging fromabout 4° C. to about 72° C., from about 16° C. to about 70° C., fromabout 37° C. to about 50° C., from about 40° C. to about 45° C., fromabout 30° C. to about 42° C., from about 25° C. to about 42° C., fromabout 25° C. to about 30° C., from about 28° C. to about 32° C., fromabout 29° C. to about 31° C. In some instances, the temperature is about15° C., about 16° C., about 17° C., about 18° C., about 19° C., about20° C., about 21° C., about 22° C., about 23° C., about 24° C., about25° C., about 26° C., about 27° C., about 28° C., about 29° C., about30° C., about 31° C., about 32° C., about 33° C., about 34° C., about35° C., about 36° C., about 37° C., about 38° C., about 39° C., about40° C., about 41° C., about 42° C., about 43° C., about 44° C., about45° C., about 46° C., about 47° C., about 48° C., about 49° C., about50° C., about 51° C., about 52° C., about 53° C., about 54° C., about55° C., about 56° C., about 57° C., about 58° C., about 59° C., about60° C., about 61° C., about 62° C., about 63° C., about 64° C., about65° C., about 66° C., about 67° C., about 68° C., about 69° C., about70° C., about 71° C., about 72° C., about 73° C., about 74° C., or about75° C. In some instances, the temperature is about or at most about 42°C. In some instances, the temperature is about or at most about 50° C.In some instances, the temperature is about or at most about 35° C. Insome instances, the temperature is about or at most about 25° C. In someinstances, the temperature is about or at most about 30° C. In someinstances, the reaction is incubated from about 20 minutes to about 3hours, from about 30 minutes to about 1.5 hours, from about 30 minutesto about 1 hour, from about 30 minutes to about 2 hours, from about 1hour to about 2 hours, from about 1 hour to about 1.5 hours, from about30 minutes to about 5 hours, from about 1 hour to about 3 hours, fromabout 1 hour to about 4 hours, from about 1 hour to about 5 hours. Insome instances, the reaction is incubated for about 1 hour. In someinstances, the reaction is incubated for about 20 minutes, about 30minutes, about 40 minutes, about 50 minutes, about 1 hour, about 1.5hours, about 2 hours, about 2.5 hours, about 3 hours, about 3.5 hours,about 4 hours, about 4.5 hours, or about 5 hours. In some instances, thereaction is incubated for at least at least about 20 minutes, at leastabout 30 minutes, at least about 40 minutes, at least about 50 minutes,at least about 1 hour, at least about 1.5 hours, at least about 2 hours,at least about 2.5 hours, at least about 3 hours, at least about 3.5hours, at least about 4 hours, at least about 4.5 hours, or at leastabout 5 hours. In some instances, the reaction is incubated at about 30°C. for about 1 hour, or at about 42° C. for about 1 hour. In someinstances, the conditions sufficient for generating a molecule or anucleic acid molecule comprises a temperature of about 12° C. to about42° C. for about 1 minute to about 5 hours. In some instances, theconditions sufficient for generating a molecule or a nucleic acidmolecule comprises a temperature of about 8° C. to about 50° C. forabout 1 minute to about 24 hours.

In some instances, a primer can be designed to be a certain length. Insome instances, a primer can be from about 6 to about 100 nucleotides,from about 6 to about 90 nucleotides, from about 6 to about 80nucleotides, from about 6 to about 70 nucleotides, from about 6 to about60 nucleotides, from about 6 to about 50 nucleotides, from about 6 toabout 40 nucleotides, from about 6 to about 30 nucleotides, from about 6to about 20 nucleotides, or from about 6 to about 10 nucleotides inlength. In some instances, a primer can be from about 25 to about 80,from about 25 to about 75, from about 25 to about 70, from about 25 toabout 65, from about 25 to about 60, from about 25 to about 55, fromabout 25 to about 50, from about 25 to about 45, from about 25 to about40, from about 25 to about 35, or from about 25 to about 30 bases inlength. In some instances, a primer can be at least about 5, at leastabout 6, at least about 7, at least about 8, at least about 9, at leastabout 10, at least about 11, at least about 12, at least about 13, atleast about 14, at least about 15, at least about 16, at least about 17,at least about 18, at least about 19, at least about 20, at least about25, at least about 30, at least about 35, at least about 40, at leastabout 45, at least about 50, at least about 55, at least about 60, atleast about 65, at least about 70, at least about 75, at least about 80,at least about 85, at least about 90, at least about 95 or at leastabout 100 bases in length. In some instances, a primer can be about 5,about 6, about 7, about 8, about 9, about 10, about 11, about 12, about13, about 14, about 15, about 16, about 17, about 18, about 19, about20, about 25, about 30, about 35, about 40, about 45, about 50, about55, about 60, about 65, about 70, about 75, about 80, about 85, about90, about 95 or about 100 bases in length. In some instances, a primercan be at least about, no more than about, or about 120, 130, 140, 150,160, 170, 180, 190, 200, 230, 250, 270, 290, 300, 320, 340, 350, 370,400, 420, 450, 470, 490, or 500.

In some instances, a primer can be designed to anneal to a target at agiven melting temperature (Tm). In some instances, a Tm can be fromabout 20° C. to about 100° C., about 20° C. to about 90° C., about 20°C. to about 80° C., about 20° C. to about 70° C., about 20° C. to about60° C., about 20° C. to about 50° C., about 20° C. to about 40° C., orabout 20° C. to about 30° C. In some instances, a Tm can be at leastabout, at most about, or about 20° C., 21° C., 22° C., 23° C., 24° C.,25° C., 26° C., 27° C., 28° C., 29° C., 30° C., 31° C., 32° C., 33° C.,34° C., 35° C., 36° C., 37° C., 38° C., 39° C., 40° C., 41° C., 42° C.,43° C., 44° C., 45° C., 46° C., 47° C., 48° C., 49° C., 50° C., 51° C.,52° C., 53° C., 54° C., 55° C., 56° C., 57° C., 58° C., 59° C., 60° C.,61° C., 62° C., 63° C., 64° C., 65° C., 66° C., 67° C., 68° C., 69° C.,70° C., 71° C., 72° C., 73° C., 74° C., 75° C., 76° C., 77° C., 78° C.,79° C., 80° C., 81° C., 82° C., 83° C., 84° C., 85° C., 86° C., 87° C.,88° C., 89° C., 90° C., 91° C., 92° C., 83° C., 84° C., 85° C., 96° C.,97° C., 98° C., 99° C., or 100° C. A plurality of primers can bedesigned to have Tms within a range, e.g., within a range spanning 15°C., 10° C., 9° C., 8° C., 7° C., 6° C., 5° C., 4° C., 3° C., 2° C., or1° C. A plurality of primers can be designed to have identical Tms.

In some instances the enzyme, or modified enzyme (e.g., modified reversetranscriptase), or protein, or polypeptide, or a variant, or a PCRproduct, or a cDNA molecule, or a template, or a nucleic acid molecule,or any component of the present disclosure may be purified. In someinstances, the fragmented or degraded nucleic acid (e.g., RNA or DNA)may be purified. In some instances, the reverse transcriptase or amodified reverse transcriptase may be purified. In some instances, theR2 reverse transcriptase or a modified R2 reverse transcriptase may bepurified. In some instances, the non-LTR retrotransposon protein orpolypeptide having reverse transcriptase activity, or a modified non-LTRretrotransposon protein or a modified polypeptide having reversetranscriptase activity may be further purified. In some instances, thecDNA molecule may be purified. In some instances, the template may bepurified. In some instances, the acceptor nucleic acid molecule may bepurified.

Purification may comprise precipitation, ultracentrifugation,chromatographic method based on size, charge, hydrophobicity, affinity,metal binding, HPLC. In some instances, the purification comprisescolumn chromatography. In some instances, the column chromatography maybe size exclusion (SEC), ion exchange (IEX), affinity chromatography,immobilized metal ion affinity chromatography (IMAC), Ni-IMACchromatography, and/or hydrophobic interaction (HIC). In some instances,the purification comprises His-tag affinity resin. In some instances,the purification may comprise one step. In some instances, thepurification may comprise two steps. In some instances, the two steppurification comprises nickel and heparin. In some instances, the twostep purification comprises nickel and heparin affinity purifications.In some instances, the two purification steps provide higher activityand/or increased template jumping compared to one step purification. Insome instances, the purification comprises heparin-affinitypurification. In some instances, purification may include affinitypurification, Ni-NTA affinity, fast protein liquid chromatography (FPLC)(e.g., AKTA and Bio-Rad FPLC systems), high-pressure liquidchromatography (HPLC) (e.g., Beckman and Waters HPLC). In someinstances, purification may include, but not limited to, ion exchangechromatography (e.g., Q, S), size exclusion chromatography, saltgradients, affinity purification (e.g., Ni, Co, FLAG, maltose,glutathione, protein A/G), gel filtration, reverse-phase, ceramic HYPERD(Registered trademark) ion exchange chromatography, and hydrophobicinteraction columns (HIC). Also included are analytical methods such asSDS-PAGE (e.g., coomassie, silver stain), immunoblot, Bradford, andELISA, which may be utilized during any step of the production orpurification process, typically to measure the purity of the protein orenzyme composition.

In some instances, the overall activity of the purified enzyme, protein,polypeptide, the R2 reverse transcriptase, the non-LTR retrotransposonprotein or polypeptide having reverse transcriptase activity, thereverse transcriptase, or variants thereof, or products thereof using atwo-step purification is at least about 2%, at least about 5%, at leastabout 7%, at least about 10%, at least about 15%, at least about 20%, atleast about 25%, at least about 30%, at least about 35%, at least about40%, at least about 45%, at least about 50%, at least about 55%, atleast about 60%, at least about 65%, at least about 70%, at least about75%, at least about 80%, at least about 85%, at least about 90%, atleast about 95%, at least about 98%, at least about 99% higher than theoverall activity using the one-step purification. In some instances, theoverall activity of the purified enzyme, protein, polypeptide, the R2reverse transcriptase, the non-LTR retrotransposon protein orpolypeptide having reverse transcriptase activity, the reversetranscriptase, or variants thereof, or products thereof is at leastabout 0.5%, at least about 1%, at least about 1.5%, at least about 2%,at least about 5%, at least about 7%, at least about 10%, at least about15%, at least about 20%, at least about 25%, at least about 30%, atleast about 35%, at least about 40%, at least about 45%, at least about50%, at least about 55%, at least about 60%, at least about 65%, atleast about 70%, at least about 75%, at least about 80%, at least about85%, at least about 90%, at least about 95%, at least about 98%, atleast about 99% higher than the overall activity of the non-purifiedenzyme, protein, polypeptide, R2 reverse transcriptase, non-LTRretrotransposon protein or polypeptide having reverse transcriptaseactivity, reverse transcriptase, or variants thereof, or productsthereof. In some instances, a purified enzyme, protein, polypeptide, R2reverse transcriptase, the non-LTR retrotransposon protein, orpolypeptide having reverse transcriptase activity, reversetranscriptase, modified enzyme, modified reverse transcriptase, modifiedpolypeptide having reverse transcriptase activity, or variants thereof,or products thereof is at least about 0.5%, at least about 1%, at leastabout 3%, at least about or about 5%, at least about or about 10%, atleast about or about 15%, at least about or about 20%, at least about orabout 25%, at least about or about 30%, at least about or about 35%, atleast about or about 40%, at least about or about 45%, at least about orabout 50%, at least about or about 55%, at least about or about 60%, atleast about or about 61%, at least about or about 62%, at least about orabout 63%, at least about or about 64%, at least about or about 65%, atleast about or about 66%, at least about or about 67%, at least about orabout 68%, at least about or about 69%, at least about or about 70%, atleast about or about 71%, at least about or about 72%, at least about orabout 73%, at least about or about 74%, at least about or about 75%, atleast about or about 76%, at least about or about 77%, at least about orabout 78%, at least about or about 79%, at least about or about 80%, atleast about or about 81%, at least about or about 82%, at least about orabout 83%, at least about or about 84%, at least about or about 85%, atleast about or about 86%, at least about or about 87%, at least about orabout 88%, at least about or about 89%, at least about or about 90%, atleast about or about 91%, at least about or about 92%, at least about orabout 93%, at least about or about 94%, at least about or about 95%, atleast about or about 96%, at least about or about 97%, at least about orabout 98%, or at least about or about 99% pure.

In some instances, the purified enzyme, protein, polypeptide, R2 reversetranscriptase, non-LTR retrotransposon protein or polypeptide havingreverse transcriptase activity, reverse transcriptase, or variantsthereof, or products thereof produces template jumping that is at leastabout or about one time, at least about or about two times, at leastabout or about three times, at least about or about four times, at leastabout or about five times, at least about or about six times, at leastabout or about seven times, at least about or about eight times, atleast about or about nine times, at least about or about ten times, atleast about or about fifteen times, at least about or about twentytimes, at least about or about twenty five times, at least about orabout thirty times, at least about or about forty times, at least aboutor about fifty times, at least about or about seventy times, at leastabout or about eighty times, at least about or about ninety times, atleast about or about 100 times, at least about or about 150 times, atleast about or about 200 times, at least about or about 250 times, atleast about or about 300 times, at least about or about 350 times, atleast about or about 400 times, at least about or about 500 times, atleast about or about 700 times, at least about or about 1000 times, atleast about or about 10000 times more and/or higher intensity than thenon-purified enzyme, protein, polypeptide, R2 reverse transcriptase,non-LTR retrotransposon protein or polypeptide having reversetranscriptase activity, reverse transcriptase, or variants thereof, orproducts thereof.

Mutation of Enzymes

In some instances, a modified enzyme, or derivatives and variants may beprepared during synthesis of the peptide or by post-productionmodification. In some instances, a modified enzyme, or derivatives andvariants may be produced by site-directed mutagenesis (e.g. Q5®Site-Directed Mutagenesis Kit Protocol), random mutagenesis, orenzymatic cleavage and/or ligation of nucleic acids. In some instances,the derivatives and variants, or a modified enzyme are produced byrandom mutagenesis. In some instances, a rational design and/ormutagenesis is based on sequence alignment analysis. In some instances,the rational design/mutagenesis is based on sequence alignment analysiswith defined and known enzymes and proteins. In some instances, sequencealignment analysis or homology modeling is performed with enzymes and/orelements with homology to R2, including, but not limited to, non-LTRretrotransposons, telomerase, group II introns, LTR retrotransposons,reverse transcriptase, retroviral reverse transcriptase (e.g., HIV,MMLV), and viral RNA dependent RNA polymerase.

In some instances, variants or modified enzymes of the presentdisclosure can be produced by, including, but not limited to, forexample, site-saturation mutagenesis, scanning mutagenesis, insertionalmutagenesis, deletion mutagenesis, random mutagenesis, site-directedmutagenesis, and directed-evolution, as well as various otherrecombinatorial approaches. Methods for making modified enzymes,polynucleotides and proteins (e.g., variants) include DNA shufflingmethodologies, methods based on non-homologous recombination of genes,such as ITCHY (See, Ostermeier et al., 7:2139-44 [1999]), SCRACHY (See,Lutz et al. 98:11248-53 [2001]), SHIPREC (See, Sieber et al., 19:456-60[2001]), and NRR (See, Bittker et al., 20:1024-9 [2001]; Bittker et al.,101:7011-6 [2004]), and methods that rely on the use of oligonucleotidesto insert random and targeted mutations, deletions and/or insertions(See, Ness et al., 20:1251-5 [2002]; Coco et al., 20:1246-50 [2002]; Zhaet al., 4:34-9 [2003]; Glaser et al., 149:3903-13 [1992]). In someinstances, polynucleotides, polypeptides, proteins, or enzymes of thepresent disclosure may be altered by being subjected to randommutagenesis by error-prone PCR, random nucleotide insertion or othermethods prior to recombination. Polynucleotides, polypeptides, proteins,or enzymes of the present disclosure may be produced by DNA shuffling,gene-shuffling, motif-shuffling, exon-shuffling, and/or codon-shuffling(collectively referred to as “DNA shuffling”). DNA shuffling involvesthe assembly of two or more DNA segments by homologous or site-specificrecombination to generate variation in the polynucleotide sequence. DNAshuffling may be employed to modulate the activities of polynucleotides,polypeptides, proteins, or enzymes of the present disclosure, suchmethods can be used to generate polypeptides with altered activity. See,generally, U.S. Pat. Nos. 5,605,793; 5,811,238; 5,830,721; 5,834,252;5,837,458; and 6,444,468; and Patten et al., Curr. Opinion Biotechnol.8:724-33 (1997); Harayama, Trends Biotechnol. 16(2):76-82 (1998);Hansson, et al., J. Mol. Biol. 287:265-76 (1999); and Lorenzo andBlasco, Biotechniques 24(2):308-13 (1998). Polynucleotides,polypeptides, proteins, or enzymes of the present disclosure may containone or more components, motifs, sections, parts, domains, fragments,etc., of a polynucleotide, polypeptide, protein, or enzyme of thepresent disclosure. In some instances, kits for use in mutagenic PCR,such as, for example, the Diversify PCR Random Mutagenesis Kit(Clontech) or the GeneMorph Random Mutagenesis Kit (Stratagene) may beused.

In some instances, variant proteins differ from a parent protein ormodified enzymes differ from a wild-type or unmodified enzyme and oneanother by a small number of amino acid residues. The number ofdiffering amino acid residues may be one or more, preferably about 1, 2,3, 4, 5, 10, 15, 20, 30, 40, 50, 60, 70, 80, 90, 100 or more amino acidresidues. In some instances, the number of different amino acids betweenvariants is between about 1 and about 10. In some instances, relatedproteins and particularly variant proteins comprise at least about 35%,40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, or99% amino acid sequence identity. Additionally, a related protein or avariant protein as used herein, refers to a protein that differs fromanother related protein or a parent protein in the number of prominentregions. For example, in some instances, variant proteins have about 1,2, 3, 4, 5, 6, 7, 8, 9, or 10 corresponding prominent regions thatdiffer from the parent protein.

In some instances, screening methods can include conventional screeningmethods such as liquid phase, or microtiter plate based assays. Theformat for liquid phase assays is often robotically manipulated 96, 384,or 1536-well microtiter plates. Other screening methods include growthselection (Snustad et al., 1988; Lundberg et al., 1993; Yano et al.,1998), colorimetric screening of bacterial colonies or phage plaques(Kuritz, 1999), in vitro expression cloning (King et al., 1997) and cellsurface or phage display (Benhar, 2001). In some instances, screeningapproaches may be a method selected from yeast-2-hybrid, n-hybrid,reverse-2-hybrid, reverse n-hybrid, split two hybrid, bacterial display,phage display, retroviral display, ribosome display, covalent display,in vitro display, or any other display method. In some instances, thelibrary is screened using a phage display method.

Analysis of the sequences derived from template jumps: the bandcorresponding to the template jump product may be excised from apolyacrylamide gel, eluted with sodium acetate (e.g. 0.3 M sodiumacetate, pH 5.2), SDS (e.g. 0.03%) for several hours at roomtemperature, phenol/chloroform extracted and ethanol precipitated. Theisolated cDNA may then be used as a template for PCR amplification usingone or more primer(s). The PCR products may then be directly cloned intoa vector (Burke et al., “R4, a non-LTR Retrotransposon Specific to theLarge Subunit rRNA Gene of Nematodes,” Nucleic Acids Res. 23: 4628-4634(1995)) and individual clones sequenced.

In some instances, the variants or modified enzymes or non-naturallyoccurring enzymes or modified polypeptides have/has improved enzymeproperty compared to the unmodified, wild type or naturally occurringenzyme or polypeptide. In some instances, the improved enzyme propertyis selected from at least one of the following: increased stability(e.g., increased thermostability), increased specific activity,increased protein expression, improved purification, improvedprocessivity, improved strand displacement, increased template jumping,improved ssDNA priming, and improved fidelity. In some instances, theterm stability may include, but it is not limited to, thermal stability,storage stability, and pH stability. In some instances, specificactivity is a measurement of the enzymatic activity (in units) of theprotein or enzyme relative to the total amount of protein or enzyme usedin a reaction. In some instances, specific activity is measured based onthe ability of the enzyme to produce cDNA molecule. In some instances,the specific activity is measured in U/mg protein determined based on aprimer extension reaction. In some instances, the altered or improvedproperty may be characterized by a Performance Index (PI), where the PIis a ratio of performance of the variant, the modified enzyme, or thenon-naturally occurring enzyme compared to the wild-type or compared toa naturally occurring enzyme or protein. The term “performance index(PI)” may refer to the ratio of performance of a variant polypeptide toa parent polypeptide or of a modified enzyme to an unmodified enzyme(e.g., reverse transcriptase) or of a non-naturally occurring enzyme toa naturally-occurring enzyme for a specified performance characteristic.In some instances, the specified performance or enzyme propertycharacteristic may include, but is not limited to, stability (e.g.,thermostability), specific activity, protein expression, purification,processivity, strand displacement, end-to-end template jumping, improvedssDNA priming, and/or fidelity. In some instances, the PI is greaterthan about 0.5, while in other instances, the PI is about 1 or isgreater than about 1. In some instances, the variant polypeptide,modified enzyme (e.g., modified reverse transcriptase), or thenon-naturally occurring enzyme comprises a modification at one or moreamino acid positions. In some instances, the modified enzyme or thenon-naturally occurring enzyme has a performance index (PI) that isequal to or greater than about 0.1, equal to or greater than about 0.2,equal to or greater than about 0.3, equal to or greater than about 0.4,equal to or greater than about 0.5, equal to or greater than about 0.6,equal to or greater than about 0.7, equal to or greater than about 0.8,equal to or greater than about 0.9, equal to or greater than about 1,equal to or greater than about 1.2, equal to or greater than about 1.5,equal to or greater than about 2, equal to or greater than about 2.5,equal to or greater than about 3, equal to or greater than about 3.5,equal to or greater than about 4, equal to or greater than about 4.5,equal to or greater than about 5, equal to or greater than about 5.5,equal to or greater than about 6, equal to or greater than about 6.5,equal to or greater than about 7, equal to or greater than about 8,equal to or greater than about 9, equal to or greater than about 10,equal to or greater than about 50, equal to or greater than about 75,equal to or greater than about 100, equal to or greater than about 500,equal to or greater than about 1000. In some instances, the variant ormodified enzyme has a performance index (PI) from about 0.1 to about 1,from about 0.5 to about 1, from about 0.1 to about 2, from about 1 toabout 2, from about 0.5 to about 2, from about 0.5 to about 10, fromabout 1 to about 10, from about 0.1 to about 10, from about 1 to about5, from about 0.5 to about 5, from about 0.5 to about 20, from about 0.3to about 20, from about 5 to about 10, from about 1.5 to about 10, fromabout 1.5 to about 50, from about 1 to about 50, from about 1.5 to about100, from about 1.5 to about 75, from about 4 to about 10, from 3 toabout 10, from about 3 to about 25, from about 3 to about 50, from about2 to about 20, from about 2 to about 100, from about 2 to about 1000,from about 1 to about 1000. In some instances, the performance index isdetermined for protein expression. In some instances, the performanceindex is determined for at least one characteristic that improves enzymeproperty. In some instances, the performance index is determined forpurification. In some instances, the performance index is determined forstability (e.g., thermostability). In some instances, the performanceindex is determined for specific activity. In some instances, theperformance index is determined for processivity. In some instances, theperformance index is determined for strand displacement. In someinstances, the performance index is determined for template jumping. Insome instances, the performance index is determined for fidelity. Insome instances, the characteristic that improves enzyme property isselected from the group consisting of increased thermal stability,increased specific activity, and increased protein expression. In someinstances, the performance index is performed at 30° C. In someinstances, the enzyme property is analyzed at 30° C. In some instances,the enzyme property, stability (e.g., thermostability), specificactivity, protein expression, purification, processivity, stranddisplacement, template jumping, and/or fidelity is performed at 30° C.In some instances, the performance index for measuring enzyme property,is performed at a specific temperature. In some instances, thetemperature is from about 25° C. to about 42° C. In some instances, thetemperature is from about 8° C. to about 50° C. In some instances, theperformance index for measuring enzyme property may be carried out at atemperature ranging from about from about 8° C. to about 50° C., fromabout 12° C. to about 42° C., 25° C. to about 42° C., from about 25° C.to about 40° C., from about 28° C. to about 38° C., from about 30° C. toabout 38° C., from about 35° C. to about 37° C., from about 27° C. toabout 38° C., from about 27° C. to about 37° C., from about 26° C. toabout 42° C., from about 25° C. to about 38° C., from about 27° C. toabout 38° C., from about 29° C. to about 38° C., from about 29° C. toabout 32° C. In some instances, the performance index for measuringenzyme property may be carried out at a temperature that is equal to orlower than about 8° C., equal to or lower than about 12° C., equal to orlower than about 20° C., equal to or lower than about 4° C., equal to orlower than about 55° C., equal to or lower than about 37° C., equal toor lower than about 25° C., equal to or lower than about 28° C., equalto or lower than about 30° C., equal to or lower than about 32° C.,equal to or lower than about 34° C., equal to or lower than about 35°C., equal to or lower than about 36° C., equal to or lower than about33° C., equal to or lower than about 31° C., equal to or lower thanabout 60° C., equal to or lower than about 38° C., equal to or lowerthan about 39° C., equal to or lower than about 40° C., equal to orlower than about 41° C., equal to or lower than about 42° C., equal toor lower than about 50° C. In some instances, the temperature may rangefrom about 25° C. to about 80° C.

In some instances, the specific activity of the modified enzyme is fromabout 5 units/mg to about 140,000 units/mg, from about 5 units/mg toabout 125,000 units/mg, from about 50 units/mg to about 100,000units/mg, from about 100 units/mg to about 100,000 units/mg, from about250 units/mg to about 100,000 units/mg, from about 500 units/mg to about100,000 units/mg, from about 1000 units/mg to about 100,000 units/mg,from about 5000 units/mg to about 100,000 units/mg, from about 10,000units/mg to about 100,000 units/mg, from about 25,000 units/mg to about75,000 units/mg. In some instances, the ranges of specific activitiesinclude a specific activity of from about 20,000 units/mg to about140,000 units/mg, a specific activity from about 20,000 units/mg toabout 130,000 units/mg, a specific activity from about 20,000 units/mgto about 120,000 units/mg, a specific activity from about 20,000units/mg to about 110,000 units/mg, a specific activity from about20,000 units/mg to about 100,000 units/mg, a specific activity fromabout 20,000 units/mg to about 90,000 units/mg, a specific activity fromabout 25,000 units/mg to about 140,000 units/mg, a specific activityfrom about 25,000 units/mg to about 130,000 units/mg, a specificactivity from about 25,000 units/mg to about 120,000 units/mg, aspecific activity from about 25,000 units/mg to about 110,000 units/mg,a specific activity from about 25,000 units/mg to about 100,000units/mg, and a specific activity from about 25,000 units/mg to about90,000 units/mg. In some instances, the lower end of the specificactivity range may vary from 30,000, 35,000, 40,000, 45,000, 50,000,55,000, 60,000, 65,000, 70,000, 75,000, and 80,000 units/mg. In someinstances, the upper end of the range may vary from 150,000, 140,000,130,000, 120,000, 110,000, 100,000, and 90,000 units/mg.

Kits

Any of the compositions described herein may be comprised in a kit. In anon-limiting example, the kit, in a suitable container, comprises one ormore primer(s). The kit can also comprise reaction components for primerextension and amplification (e.g., dNTPs, polymerase, buffers). The kitcan include reagents for library formation (e.g., primers (probes),dNTPs, polymerase, and enzymes). The kit may also comprise approachesfor purification, such as a bead suspension. The kit can includereagents for sequencing, e.g., fluorescently labelled dNTPs, sequencingprimers, etc.

In some instances, some of the components of the kit may be packagedeither in aqueous media or in lyophilized form. The containers of thekits can include at least one vial, test tube, or other containers, intowhich a component may be placed and suitably aliquoted. Where there ismore than one component in the kit, the kit also can contain a second,third or other additional container into which the additional componentsmay be separately placed. When the components of the kit are provided inone or more liquid solutions, the liquid solution can be an aqueoussolution. The components of the kit may be provided as dried powder(s).When reagents and/or components are provided as a dry powder, the powdercan be reconstituted by the addition of a suitable solvent.

A kit can include instructions for employing the kit components as wellthe use of any other reagent not included in the kit. Instructions mayinclude variations that can be implemented.

In some instances, a kit may be used for the preparation of cDNA from atemplate (e.g. RNA template). Such a kit may include a carrier devicecompartmentalized to receive one or more containers, such as vials,tubes, and the like, each of which includes one of the separate elementsused to prepare cDNA from RNA. For example, there may be provided afirst container, the contents of which include a reverse transcriptase(e.g. non-retroviral reverse transcriptase, non-LTR retrotransposon, R2reverse transcriptase) or variants thereof, in a liquid solution, powderform, or lyophilized form. Further, any number of additional containerscan be provided, the contents of which independently include suitablebuffers, substrates for nucleotide synthesis such as the deoxynucleotidetriphosphates (e. g., dATP, dCTP, dGTP, and dTTP) either individually orcollectively in a suitable solution, a template (e.g. template RNA), oneor more primer(s), and acceptor nucleic acid molecule (e.g. acceptorRNA), and optionally a terminal transferase in solution. In someinstances, a kit may comprise a fragment or degraded nucleic acid, DNA,RNA, or a combination thereof, one of more primer(s), an acceptornucleic acid molecule (e.g., an acceptor nucleic acid moleculecomprising a modified nucleotide), a reverse transcriptase (e.g.,non-retroviral reverse transcriptase, non-LTR retrotransposon, R2reverse transcriptase) or variants thereof, suitable buffers, substratesfor nucleotide synthesis such as the deoxynucleotide triphosphates (e.g., dATP, dCTP, dGTP, and dTTP). Any combinations of the abovecomponents can be provided. Any of the above components may be excludedfrom the kit. In some instances, the one or more primer(s) may be one ormore random primer(s). In some instances, any of the components may beindividually packed.

The present disclosure relates to a kit of producing a nucleic acidmolecule (e.g., cDNA molecule) comprising: one or more primer(s),nucleotides, at least one modified reverse transcriptase, a template,and instructions for performing any of the methods disclosed in thepresent disclosure. In some instances, a kit can be used for detectingnucleic acid comprising a nucleic acid template (e.g., a DNA template),at least one modified reverse transcriptase, nucleotides, andinstructions for performing any of the methods disclosed in the presentdisclosure. In some instances, the modified reverse transcriptasepresent in the kit or to be used with the kit has activity and/or iscapable of template jumping at a temperature equal to or less than aboutor more than about 4° C., 8° C., 12° C., 13° C., 14° C., 15° C., 16° C.,17° C., 18° C., 19° C., 20° C., 21° C., 22° C., 23° C., 24° C., 25° C.,26° C., 27° C., 28° C., 29° C., 30° C., 31° C., 32° C., 33° C., 34° C.,35° C., 36° C., 37° C., 38° C., 39° C., 40° C., 41° C., 42° C., 45° C.,46° C., 47° C., 48° C., 49° C., 50° C., 52° C., 55° C., or 60° C. Insome instances, the nucleic acid and/or the template (e.g., nucleic acidtemplate, DNA, or RNA) is present at a concentration as low as about 50femtomolar, as low as about 60 femtomolar, as low as about 70femtomolar, as low as about 75 femtomolar, as low as about 80femtomolar, as low as about 90 femtomolar, as low as about 100femtomolar, as low as about 120 femtomolar, as low as about 150femtomolar, as low as about 200 femtomolar, as low as about 250femtomolar, as low as about 300 femtomolar, as low as about 350femtomolar, as low as about 400 femtomolar, as low as about 500femtomolar, as low as about 550 femtomolar, as low as about 600femtomolar, as low as about 700 femtomolar, or as low as about 800femtomolar. In some instances, the nucleic acid and/or the template(e.g., nucleic acid template, DNA, or RNA) is present at a concentrationas high as 1 micromolar. In some instances, a kit may comprise one ormore primer(s), and/or a template annealed to a primer. The presentdisclosure also relates to a kit of producing modified enzymes, modifiedreverse transcriptases, or modified polypeptides. In some instances, thekit includes a PCR step and/or components to use for PCR.

In some instances, the present disclosure relates to a kit for detectingnucleic acid comprising a template, at least one modified reversetranscriptase, nucleotides, and instructions to perform the method ofthe present disclosure. In some instances, the nucleic acid is presentat a concentration of at least about 50 femtomolar, at least about 20femtomolar, at least about 100 femtomolar, or greater than about 1000femtomolar.

Sequencing

In some instances, determining the number of different labeled nucleicacids may comprise determining the sequence of the labeled nucleic acidor any product thereof (e.g., labeled-amplicons, labeled-cDNAmolecules). In some instances, an amplified target nucleic acid may besubjected to sequencing. Determining the sequence of the labeled nucleicacid or any product thereof may comprise conducting a sequencingreaction to determine the sequence of at least a portion of the sampletag, molecular identifier label, at least a portion of the labelednucleic acid, a complement thereof, a reverse complement thereof, or anycombination thereof. In some instances, only the sample tag or a portionof the sample tag is sequenced. In some instances, only the molecularidentifier label or a portion of the molecular identifier label issequenced.

Determining the sequence of the labeled nucleic acid or any productthereof may be performed by sequencing methods such as Helioscope(Registered Trademark) single molecule sequencing, Nanopore DNAsequencing, Lynx Therapeutics' Massively Parallel Signature Sequencing(MPSS), 454 pyrosequencing, Single Molecule real time (RNAP) sequencing,Illumina (Solexa) sequencing, SOLiD sequencing, Ion Torrent, Ionsemiconductor sequencing, Single Molecule SMRT (Registered Trademark)sequencing, Polony sequencing, DNA nanoball sequencing, and VisiGenBiotechnologies approach. Alternatively, determining the sequence of thelabeled nucleic acid or any product thereof may use sequencingplatforms, including, but not limited to, Genome Analyzer Ix, HiSeq, andMiSeq offered by Illumina, Single Molecule Real Time (SMRT (RegisteredTrademark)) technology, such as the PacBio RS system offered by PacificBiosciences (California) and the Solexa Sequencer, True Single MoleculeSequencing (tSMS (Registered Trademark)) technology such as theHeliScope (Registered Trademark) Sequencer offered by Helicos Inc.(Cambridge, Mass.). In some instances, the sequencing reaction can occuron a solid or semi-solid support, in a gel, in an emulsion, on asurface, on a bead, in a drop, in a continuous follow, in a dilution, orin one or more physically separate volumes.

Sequencing may comprise sequencing at least about 10, 20, 30, 40, 50,60, 70, 80, 90, 100 or more nucleotides or base pairs of the labelednucleic acid. In some instances, sequencing comprises sequencing atleast about 200, 300, 400, 500, 600, 700, 800, 900, 1000 or morenucleotides or base pairs of the labeled nucleic acid. In otherinstances, sequencing comprises sequencing at least about 1500; 2,000;3,000; 4,000; 5,000; 6,000; 7,000; 8,000; 9,000; or 10,000 or morenucleotides or base pairs of the labeled nucleic acid.

Sequencing may comprise at least about 200, 300, 400, 500, 600, 700,800, 900, 1000 or more sequencing reads per run. In some instances,sequencing comprises sequencing at least about 1500; 2,000; 3,000;4,000; 5,000; 6,000; 7,000; 8,000; 9,000; or 10,000 or more sequencingreads per run. Sequencing may comprise less than or equal to about1,600,000,000 sequencing reads per run. Sequencing may comprise lessthan or equal to about 200,000,000 reads per run.

Cells

The cell as described in the present disclosure may be a cell from ananimal (e.g., human, rat, pig, horse, cow, dog, mouse). In someinstances, the cell may be a single cell. In some instances, the cell isa human cell. The cell may be a fetal human cell. The fetal human cellmay be obtained from a mother pregnant with the fetus. The cell may be acell from a pregnant mother. The cell may be a cell from a vertebrate,invertebrate, fungi, archaea, or bacteria. The cell may be from amulticellular tissue (e.g., an organ (e.g., brain, liver, lung, kidney,prostate, ovary, spleen, lymph node, thyroid, pancreas, heart, skeletalmuscle, intestine, larynx, esophagus, and stomach), a blastocyst). Thecell may be a cell from a cell culture. The cell may be a HeLa cell, aK562 cell, a Ramos cell, a hybridoma, a stem cell, an undifferentiatedcell, a differentiated cell, a circulating cell, a CHO cell, a 3T3 cell,and the like.

Circulating diseased cells that can be used in the methods of thepresent disclosure include all types of circulating cells that may beaffected by a disease or condition or infected by an infectious agent. Acirculating cell refers to a cell present in the bodily fluid. Acirculating cell may not necessarily circulate throughout the entirebody or in the circulatory system. For example, a circulating cell maybe present locally, such as in synovial fluid, or cerebrospinal fluid,or lymph fluid. A circulating diseased cell may also be detached from atissue or organ that has been affected by a disease or condition orinfected by an infectious agent. In other instances, the circulatingdiseased cells can be a mixture of different types of circulatingdiseased cells.

In some instances, the cell is a cancerous cell. Non-limiting examplesof cancer cells may include a prostate cancer cell, a breast cancercell, a colon cancer cell, a lung cancer cell, a brain cancer cell, andan ovarian cancer cell. In some instances, the cell is from a cancer(e.g., a circulating tumor cell). Non-limiting examples of cancers mayinclude, adenoma, adenocarcinoma, squamous cell carcinoma, basal cellcarcinoma, small cell carcinoma, large cell undifferentiated carcinoma,chondrosarcoma, and fibrosarcoma.

In some instances, the cell is a rare cell. A rare cell can be acirculating tumor cell (CTC), circulating epithelial cell (CEC),circulating stem cell (CSC), stem cells, undifferentiated stem cells,cancer stem cells, bone marrow cells, progenitor cells, foam cells,fetal cells, mesenchymal cells, circulating endothelial cells,circulating endometrial cells, trophoblasts, immune system cells (hostor graft), connective tissue cells, bacteria, fungi, or pathogens (forexample, bacterial or protozoa), microparticles, cellular fragments,proteins and nucleic acids, cellular organelles, other cellularcomponents (for example, mitochondria and nuclei), and viruses.

In some instances, the cell is from a tumor. In some instances, thetumor is benign or malignant. The tumor cell may comprise a metastaticcell. In some instances, the cell is from a solid tissue that comprisesa plurality of different cell types (e.g., different genotypes).

Samples

In some instances, the sample that includes the template nucleic acid,e.g. DNA and/or RNA, may be combined into the reaction mixture in anamount sufficient for producing a product. In some instances, the sampleis combined into the reaction mixture such that the final concentrationof DNA and/or RNA in the reaction mixture is from about 1 fg/μL to about10 μg/L, from about 1 μg/μL to about 5 μg/μL, from about 0.001 μg/L toabout 2.5 μg/μL, from about 0.005 μg/L to about 1 μg/L, from about 0.01μg/μL to about 0.5 μg/L, from about 0.1 μg/L to about 0.25 μg/L. In someinstances, the sample that includes the template is isolated from asingle cell. In some instances, the sample that includes the template isisolated from about 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, 100, 500 or morecells.

In some instances, the template is DNA, RNA, or a combination of DNA andRNA. In some instances, the template is a fragment or degraded DNA, afragment or degraded RNA, or a combination of fragment or degraded DNAand fragment or degraded RNA. In some instances, the total amount oftemplate is the total amount of template in a sample. In some instances,the total amount of template is the total amount of template in areaction mixture. In some instances, the total amount of template is thetotal amount of template in one pot or a single vessel. In someinstances, the total amount of template is the total amount of templatein one pot or a single vessel reaction. In some instances, the totalamount of the template is from about 1 femtomolar (fM) to about 100micromolar, from about 0.0001 micromolar to about 0.01 micromolar, fromabout 0.0001 micromolar to about 0.1 micromolar, from about 40femtomolar to about 0.01 micromolar, from about 50 femtomolar to about500 femtomolar, from about 50 femtomolar to about 0.01 micromolar, fromabout 50 femtomolar to about 0.1 micromolar, from about 50 femtomolar toabout 500 picomolar, from about 50 femtomolar to about 500 nanomolar,from about 50 femtomolar to about 500 micromolar, from about 50femtomolar to about 1 picomolar, from about 40 femtomolar to about 1nanomolar, from about 1 femtomolar to about 1 picolomar. In someinstances, the total amount of template is equal to or at least about orlower than about 1000 micromolar, equal to or at least about or lowerthan about 500 micromolar, equal to or at least about or lower thanabout 250 micromolar, equal to or at least about or lower than about 100micromolar, equal to or at least about or lower than about 50micromolar, equal to or at least about or lower than about 25micromolar, equal to or at least about or lower than about 10micromolar, equal to or at least about or lower than about 1 micromolar,equal to or at least about or lower than about 0.1 micromolar, equal toor at least about or lower than about 0.01 micromolar, equal to or atleast about or lower than about 0.001 micromolar, equal to or at leastabout or lower than about 0.0001 micromolar, equal to or at least aboutor lower than about 2000 nanomolar, equal to or at least about or lowerthan about 500 nanomolar, equal to or at least about or lower than about250 nanomolar, equal to or at least about or lower than about 200nanomolar, equal to or at least about or lower than about 50 nanomolar,equal to or at least about or lower than about 25 nanomolar, equal to orat least about or lower than about 20 nanomolar, equal to or at leastabout or lower than about 2 nanomolar, equal to or at least about orlower than about 0.2 nanomolar, equal to or at least about or lower thanabout 0.01 nanomolar, equal to or at least about or lower than about0.001 nanomolar, equal to or at least about or lower than about 0.0001nanomolar, equal to or at least about or lower than about 3000picomolar, equal to or at least about or lower than about 500 picomolar,equal to or at least about or lower than about 250 picomolar, equal toor at least about or lower than about 300 picomolar, equal to or atleast about or lower than about 50 picomolar, equal to or at least aboutor lower than about 25 picomolar, equal to or at least about or lowerthan about 30 picomolar, equal to or at least about or lower than about3 picomolar, equal to or at least about or lower than about 0.3picomolar, equal to or at least about or lower than about 0.01picomolar, equal to or at least about or lower than about 0.001picomolar, equal to or at least about or lower than about 0.0001picomolar, equal to or at least about or lower than about 5000femtomolar, equal to or at least about or lower than about 500femtomolar, equal to or at least about or lower than about 250femtomolar, equal to or at least about or lower than about 50femtomolar, equal to or at least about or lower than about 25femtomolar, equal to or at least about or lower than about 10femtomolar, equal to or at least about or lower than about 1 femtomolar,equal to or at least about or lower than about 0.1 femtomolar, equal toor at least about or lower than about 0.01 femtomolar, equal to or atleast about or lower than about 0.001 femtomolar, equal to or at leastabout or lower than about 0.0001 femtomolar.

In some instances, the sample may be obtained from a biological sampleobtained from a subject. In some instances, a sample comprisescirculating tumor DNA sample and/or a tissue sample. In some instances,the biological sample comprises a cell-free biological sample. In someinstances, the biological sample comprises a circulating tumor DNAsample. In some instances, the biological sample comprises a biopsysample. In some instances, the biological sample comprises a tissuesample. In some instances, the biological sample comprises liquidbiopsy. In some instances, the biological sample comprises cell-freeDNA. In some instances, the biological sample can be a solid biologicalsample, e.g., a tumor sample. In some instances, a sample from a subjectcan comprise at least about 1%, at least about 5%, at least about 10%,at least about 15%, at least about 20%, at least about 25%, at leastabout 30%, at least about 35%, at least about 40%, at least about 45%,at least about 50%, at least about 55%, at least about 60%, at leastabout 65%, at least about 70%, at least about 75%, at least about 80%,at least about 85%, at least about 90%, at least about 95%, at leastabout 96%, at least about 97%, at least about 98%, at least about 99%,or at least about 100% tumor cells or nucleic acid from a tumor. Thesolid biological sample can be processed by fixation in a formalinsolution, followed by embedding in paraffin (e.g., a FFPE sample). Thesolid biological sample can be processed by freezing. Alternatively, thebiological sample can be neither fixed nor frozen. The unfixed, unfrozensample can be stored in a solution configured for the preservation ofnucleic acid. The solid biological sample can optionally be subjected tohomogenization, sonication, French press, dounce, freeze/thaw, which canbe followed by centrifugation.

In some instances, the sample can be a liquid biological sample. In someinstances, the liquid biological sample can be a blood sample (e.g.,whole blood, plasma, or serum). A whole blood sample can be subjected toseparation of cellular components (e.g., plasma, serum) and cellularcomponents by use of a Ficoll reagent. In some instances, the liquidbiological sample can be a urine sample. In some instances, the liquidbiological sample can be a perilymph sample. In some instances, theliquid biological sample can be a fecal sample. In some instances, theliquid biological sample can be saliva. In some instances, the liquidbiological sample can be semen. In some instances, the liquid biologicalsample can be amniotic fluid. In some instances, the liquid biologicalsample can be cerebrospinal fluid. In some instances, the liquidbiological sample can be bile. In some instances, the liquid biologicalsample can be sweat. In some instances, the liquid biological sample canbe tears. In some instances, the liquid biological sample can be sputum.In some instances, the liquid biological sample can be synovial fluid.In some instances, the liquid biological sample can be vomit. In someinstances, the liquid biological sample can be a cell-free sample. Insome specific instances, the cell-free sample can be a cell-free plasmasample.

Polynucleotides in a sample (which can be referred to as input nucleicacid or input) can comprise DNA. The input nucleic acid can be complexDNA, such as double-stranded DNA, genomic DNA or mixed nucleic acidsfrom more than one organism. Polynucleotides in the sample can compriseRNA. The RNA can be obtained and purified. RNA can include RNAs inpurified or unpurified form, which include, but are not limited to,mRNAs, tRNAs, snRNAs, rRNAs, retroviruses, small non-coding RNAs,microRNAs, polysomal RNAs, pre-mRNAs, intronic RNA, viral RNA, cell-freeRNA and fragments thereof. The non-coding RNA, or ncRNA may includesnoRNAs, microRNAs, siRNAs, piRNAs and long nc RNAs. Polynucleotides inthe sample can comprise cDNA. The cDNA can be generated from RNA, e.g.,mRNA. The cDNA can be single or double stranded. The input DNA can bemitochondrial DNA. The input DNA can be cell-free DNA. The cell-free DNAcan be obtained from, e.g., a serum or plasma sample. The input DNA canbe from more than one individual or organism. The input DNA can bedouble stranded or single stranded.

In some instances, samples can be collected over a period of time.Samples can be collected over regular time intervals, or can becollected intermittently over irregular time intervals. Nucleic acidsfrom different samples can be compared, e.g., to monitor progression orrecurrence of a condition or disease.

In some instances, a sample can be collected by core biopsy. In someinstances, a sample can be collected as a purified nucleic acid.Examples of such purified samples can include precipitated nucleic acidaffixed to filter paper, phenol-chloroform extractions, nucleic acidpurified by kit purification (e.g. Quigen Miniprep (RegisteredTrademark) and the like), or gel purified nucleic acid as exemplaryexamples.

The sample of the disclosure may be a sample from an animal (e.g.,human, rat, pig, horse, cow, dog, mouse). In some instances, the sampleis a human sample. The sample may be a fetal human sample. The samplemay be from a multicellular tissue (e.g., an organ (e.g., brain, liver,lung, kidney, prostate, ovary, spleen, lymph node, thyroid, pancreas,heart, skeletal muscle, intestine, larynx, esophagus, and stomach), ablastocyst). The sample may be a cell from a cell culture.

The sample may comprise a plurality of cells. The sample may comprise aplurality of the same type of cell. The sample may comprise a pluralityof different types of cells. The sample may comprise a plurality ofcells at the same point in the cell cycle and/or differentiationpathway. The sample may comprise a plurality of cells at differentpoints in the cell cycle and/or differentiation pathway. A sample maycomprise a plurality of samples.

The plurality of samples may comprise one or more malignant cell. Theone or more malignant cells may be derived from a tumor, sarcoma orleukemia.

The plurality of samples may comprise at least one bodily fluid. Thebodily fluid may comprise blood, urine, lymphatic fluid, saliva. Theplurality of samples may comprise at least one blood sample.

The plurality of samples may comprise at least one cell from one or morebiological tissues. The one or more biological tissues may be a bone,heart, thymus, artery, blood vessel, lung, muscle, stomach, intestine,liver, pancreas, spleen, kidney, gall bladder, thyroid gland, adrenalgland, mammary gland, ovary, prostate gland, testicle, skin, adipose,eye or brain.

The biological tissue may comprise an infected tissue, diseased tissue,malignant tissue, calcified tissue or healthy tissue.

In some instances, the characteristic that improves enzyme property isselected from the group consisting of increased stability (e.g.,increased thermostability), increased specific activity, increasedprotein expression, increased processivity, increased stranddisplacement, increased end-to-end template jumping, and increasedfidelity.

EXAMPLES

The following specific examples are illustrative and non-limiting. Theexamples described herein reference and provide non-limiting support tothe various embodiments described in the preceding sections.

Example 1: Expression and Purification

Small and medium scale: Expression vector pET-45b caring modified R2non-long terminal repeat (LTR) retrotransposon or one of the modified R2reverse transcriptases of SEQ ID Nos: 1-20 was transformed into E. coliBL21 (DE3). TABLE 1 below shows examples of non-naturally occurring R2enzyme variants of the present disclosure. For expression, pre-culturecan be setup in 2 ml LB with 100 μM Corbenicillin and grown overnightfor about 8 to 12 hours at room temperature. After about 8 h to 12 h,200 μL of the pre-culture can be transferred to 25 mL of anauto-induction expression media, Overnight Express TB (Novagen), andshaker-incubated at room temperature for 36 hours to 48 hours. Cellswere harvested by centrifugation at 8000×g for 10 min at 4-8° C. Thebiomass-pellet was frozen at −20° C. for a minimum of 1 h.

Purification: pellet can be re-suspended in 0.5 mL lysis buffer (0.5 mLlysis buffer per ⅙ of the biomass) and incubated for 30 minutes at roomtemperature. Lysis buffer composition: 1× BugBuster, 100 mM SodiumPhosphate, 0.1% Tween, 2.5 mM TCEP, 3 μL Protease inhibitor mix (Roche),50 μg lysozyme, 0.5 μL DNaseI (2,000 units/ml, from NEB). Afterincubation, the lysate can be mixed with equal volume (0.5 mL) ofHis-binding buffer (50 mM Sodium Phosphate pH 7.7, 1.5M Sodium Chloride,2.5 mM TCEP, 0.1% Tween, 0.03% Triton X-100, and 10 mM Imidazole) andincubated at room temperature for about 10-15 minutes. After incubation,the lysate can be centrifuged at 10000×g for about 15 min at atemperature from about 4° C. to about 8° C. Pellet can then mixed with250 μL of His-Affinity Gel (His-Spin Protein Miniprep by Zymo Research)according to manufacturer's protocol. After the binding step, theHis-Affinity Gel was washed three times with Washing buffer (50 mMSodium Phosphate pH 7.7, 750 mM Sodium Chloride, 0.1% Tween, 0.03%Triton X-100, 2.5 mM TCEP, and 50 mM Imidazole). The R2 reversetranscriptase (RT) (e.g., non-naturally occurring enzyme) can be elutedwith 150 μL of elution buffer (50 mM Sodium Phosphate pH 7.7, 300 mMSodium Chloride, 2.5 mM TCEP, 0.1% Tween, and 250 mM Imidazole) andeither used directly or frozen in 30% glycerol. This protocol can beadjusted for expression and purification of mutagenesis and forscreening. For example, a similar protocol can be adjusted to a plateformat, such as 2 mL of the Overnight Express TB (Novagen) instead of 25mL can be used, and the purification step can comprise 96 well spinplates with nickel-immobilized resin.

Result: After purification, samples can be analyzed using sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE), 4-12%polyacrylamide, Bis-Tris.

Example 2: Surrogate/Diagnostic Assays

Example of reverse transcriptase (RT) activity assay: activity assay canbe used to compare enzyme activity, active fraction, stability (e.g.,thermostability), and robustness of the non-naturally occurring enzymes.RT activity and active fraction(s) can be estimated based on primerextension assay by comparing fraction(s) of extended to non-extended DNAprimer using various template/primer and enzyme concentrations.Extension assays can be conducted with and without the addition of a DNAtrap.

Example protocol: annealed 0.2 μM template/primer with fluorescentlylabeled primer can be pre-incubated with various concentrations of R2 RT(relative to template/primer 0.1 to 4-fold) at room temperature for 20minutes. Pre-incubation conditions can include 40 mM Tris pH 7.5, 200 mMNaCl, 5 mM TCEP, and 0.1% Tween. Extension can start with the additionof MgCl₂ (5 mM, final) and dNTPs (25 μM of each, final) and optionally aDNA trap (unlabeled DNA oligo duplex at 3 μM, final, or heparin). Theaddition of trap DNA helps to estimate RT active fraction(s). Thereaction can then incubated for 10 minutes and stopped with EDTA (50 mM,final) or formamide (50%, final). The product of the reaction can thenbe analyzed with 15% PAGE-Urea. An example of a template sequence usedis rCrArG rUrCrA rGrUrC rArGrU rCrArG rUrCrA rGrUrG rCrCrA rArArU rGrCrCrUrCrG rUrCrA rUrC and of a primer is /56-FAM/TGATGACGAGGCATTTGGC.

Example of end-to-end template jumping assay: Primer extension assaywith two templates where one template is annealed to a fluorescentlylabeled primer (donor template) and the other is primer-free (acceptornucleic acid).

Example protocol: annealed 0.1 μM template/primer with fluorescentlylabeled primer (alternatively the product of the reaction can be stainedwith Syber Gold) can be pre-incubated with various concentrations of R2RT (relative to template/primer 0.1 to 4-fold) at room temperature for20 minutes. Pre-incubation conditions can include 40 mM Tris pH 7.5, 200mM NaCl, 5 mM TCEP, and 0.1% Tween. Extension can start with theaddition of MgCl₂ (5 mM, final), dNTPs (50 μM of each, final) and theacceptor nucleic acid at various concentrations (range from about 0.01μM to about 5 μM). The reaction can then be incubated for 30 min-1 h andstopped with EDTA (50 mM, final) or formamide (50%, final). The productof the reaction can be analyzed with 15% PAGE-Urea.

Templates: the templates can be generated by in vitro RNA synthesis withT7 RNA polymerase based on the DNA template generated in a PCR reactionwith two primers, one of which included a T7 promoter sequence (i.e., afirst primer). The second primer can also be used as a DNA primer in thedonor template/primer protocol. The product of the reaction can then beanalyzed with 15% PAGE-Urea. Example of materials used: template for PCRamplification pUC18 with T7 primerCTGCAGTAATACGACTCACTATAGGATCCTCTAGAGTCGACCTGC (SEQ ID NO: 24); donorprimer GCCATTCGCCATTCAGGCTGC (SEQ ID NO: 102)(used for both PCRamplification and priming at the donor RNA template); RNA template (˜190nucleotides); acceptor nucleic acid—G-block PCR templateACGGCCAGTGAATTGTAATACGACTCACTATAGGGCGAATTGGGTACCGCCTCGAGGTCGACGGTATCGATAAGCTTGATATCGAATTCCTGCAGCGGATCCACTAGTTCTAGAGCGGCCGCCACCGCGGTGGAGCTCCAGCTTTTGTTCCCTTTAGTGAGGGTTAATTTCGAGCTTGGCGTAATCATGGTCATAGCTGTTTCC (SEQ ID NO: 103); two primers for PCRamplification (a T7 primer ACGGCCAGTGAATTGTAATACGAC (SEQ ID NO: 104) anda second primer GGAAACAGCTATGACCATG (SEQ ID NO: 105)).

Example of processivity assay: processivity of each non-naturallyoccurring enzyme can be analyzed based on primer extension and productformation using a 15% PAGE-Urea, or a 1.2% agarose gel, or a 2% agarosegel. Product length distribution can be analyzed with densitometry.

Example protocol: annealed 0.05-0.1 μM template/primer withfluorescently labeled primer (alternatively product of the reaction canbe stained with Syber Gold) can be pre-incubated with variousconcentration of R2 RT (0.1 to 4-fold relative to template/primer) for20 minutes at room temperature. Pre-incubation conditions: 40 mM Tris pH7.5, 200 mM NaCl, 5 mM TCEP, and 0.1% Tween. Extension can start withaddition of MgCl₂ (5 mM, final), dNTPs (50 μM of each, final), andoptionally a DNA trap (unlabeled DNA oligo duplex at 3 μM, final). Thereaction can then be incubated for 30 min-1 h and stopped with EDTA (50mM, final) or formamide (50%, final).

Templates: the templates can be generated by in vitro RNA synthesis withT7 RNA polymerase based on the DNA template generated in a PCR reactionwith two primers, one of which included a T7 promoter sequence. Thesecond primer can also be used as a DNA primer in the donortemplate/primer protocol. The product of the reaction was analyzed witha 15% PAGE-Urea, or a 1.2% agarose gel, or a 2% agarose gel. Materialsincluded: template for PCR amplification pUC18 with T7 primerCTGCAGTAATACGACTCACTATAGGATCCTCTAGAGTCGACCTGC, RT primerCAGGGTTATTGTCTCATGAGCG (SEQ ID NO: 101)(used for both PCR amplificationand priming at the donor RNA template), and RNA template (˜600nucleotides).

Example of Random priming: Longer RNA template(s) with several primerswith adapters or random primers with adapters; product analysis isperformed after PCR amplification to compare product's lengthdistribution (one primer is specific to the 5′-end of the template andthe second primer is complementary to the adapter sequence).

Example 3: Activity and Template Jumping Experiment Using Synthetic RNA

Non-naturally occurring R2 enzymes can have template jumping properties.

Example protocol: reactions containing 0.25 mM of dNTPs, R2 buffer, 0.4μM template/primer, acceptor nucleic acid (0 to 1 μM), non-naturallyoccurring R2, and H₂O can be used to detect template jumping. Thereactions containing the R2 enzyme or the R2 buffer can be incubated at30° C. for 1 hour. Products can be analyzed using 15% PAGE-Urea gel.

Sequences of templates, primers, and acceptors that can be used to testtemplate jumping are shown below:

P173 (RNA template) CAGUCAGUCAGUCAGUCAGUGCCAAAUGCCUCGUCAUC (SEQ ID NO: 98) P174 (fluorescently/56-FAM/TGATGACGAGGCATTTGGC (SEQ ID NO: 99) labeled primer)P181 (acceptor GTTAATAACGAAATGAGCAGCCrGrGrG (SEQ ID NO: nucleic acid)100)

Example 4: DNA Fragments can be Captured and Tagged with Non-NaturallyOccurring R2 Enzyme

This experiment can be used to show that a 200 bp DNA fragment (typicalsize for cfDNA) can be captured and tagged in a 1-pot (single vessel)reaction using the methods of the present disclosure. Some facts of thisexperiment: no prior knowledge of the sequence is required and the dataprovided by this experiment may meet the sensitivity requirement (atypical liquid biopsy sample has between about 10-30 ng of DNA, arequired sensitivity of 0.1% (˜10-30 μg)).

This experiment can be used to show that 1-pot (single vessel) reactioncontaining DNA fragments (200 bp PCR product prepared by heatdenaturation and quick cooling of PCR product) can be captured andtagged using a non-naturally occurring R2 enzyme (P8 variant R2 enzyme).In brief, this experiment can include two approaches: 1) capture of DNAfragment with RNA priming; and 2) capture of DNA fragment using RNAdonor. Briefly, the reactions per the first approach (RNA priming) caninclude H₂O, 5×R2 buffer, 0.25 mM dNTPs, 200 bp DNA fragment (0 ng (noDNA template control (NTC)), 160 μg, 32 μg, or 6 μg of DNA template),enzyme (e.g., 0.023 μg/μL P8 variant R2 enzyme), and 0.5 μM of P173. Thereactions per the second approach (RNA donor) can include H₂O, 5×R2buffer, 0.25 mM dNTPs, 200 bp DNA fragment (0 ng (no DNA templatecontrol (NTC)), 160 μg, 32 μg, or 6 μg), enzyme (e.g., 0.023 μg/L P8variant R2 enzyme), and 0.2 μM RNA donor (P173+P174). The reactions canthen be incubated at 30° C. for about 1 hour. The reactions can then bediluted 1:10 and supplemented with PCR reagents including amplificationprimers and hot-start polymerase. The PCR amplification reactions forthe first approach (RNA priming) can include H₂O, 1×taq master mix with1×SYBR Green, 0.5 μM of P169, 0.5 μM of P186, and 1× template (10 μL RTreaction in 100 μL total volume for PCR). The PCR amplificationreactions for the second approach (RNA donor) can include H₂O, 1×TaqMastermix with 1×sybr green, 0.5 μM of P169, 0.5 μM of P186, and 1×template (10 μL RT reaction in 100 μL total volume for PCR). The PCRconditions for the reactions were 95° C. for 3 minutes and 30 cycles of95° C. for 3 seconds, 54° C. for 10 seconds, and 64° C. for 10 seconds.The reactions can then be increased to 68° C. for 2′. The length of thePCR products can be confirmed on an acrylamide gel. The results can beused to show that the DNA fragment (˜200 bp) can be captured usingeither the RNA priming or the donor RNA mechanism without priorknowledge of the DNA sequence.

Sequences:

200 bp DNA CTGCAGTAATACGACTCACTATAGGATCCTCTAGAGTCGACCTG fragmentCAGGCATGCAAGCTTGGCACTGGCCGTCGTTTTACAACGTCGTG (PCR product)ACTGGGAAAACCCTGGCGTTACCCAACTTAATCGCCTTGCAGCACATCCCCCTTTCGCCAGCTGGCGTAATAGCGAAGAGGCCCGCACCGATCGCCCTTCCCAACAGTTGCGCAGCCTGAATGGCGAATGGC (SEQ ID NO: 23) P169CTGCAGTAATACGACTCACTATAGGATCCTCTAGAGTCGACCTG C (SEQ ID NO: 24) P186CAGTCAGTCAGTCAGTCAGTGCCA (SEQ ID NO: 25) P173 (RNACAGUCAGUCAGUCAGUCAGUGCCAAAUGCCUCGUCAUC (SEQ template) ID NO: 26) P174TGATGACGAGGCATTTGGC (SEQ ID NO: 27)

Example 5: Template Concatemerization

This experiment was designed to demonstrate a method for convertingshort DNA fragments into a concatemer. Concatemers may contain about 2,3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 500, 1000,or more copies of the starting nucleic acid. In brief, the initial PCRprotocol for template preparation can include H₂O, 2×Q5 master mix, P316(0.5 μM), P317 (0.5 μM), and pUC18 (0.05 ng/L). The PCR condition can be980° C. for 30 seconds followed by 30 cycles of: 980° C. for 10 seconds,660° C. for 15 seconds, and 720° C. for 10 seconds. At the end of the 30cycles, the reaction can be kept at 72° C. for 2 minutes and then, itcan be reduced to 4° C. The adaptor annealing reaction can include H₂O,Tris pH 8.0 (20 mM), NaCl (100 mM), and two primers (25 μM each;(P312+P313) or (P314+P315) or (P320+P321)). The reaction can beincubated at 900° C. for 1 minute, followed by 0.1° C./second ramp to25° C. (20 seconds) and then, it can be reduced and kept at 4° C. Thefirst adaptor ligation reaction can include H₂O (30 μL), fragmented DNA(20 μL), end repair and T-tailing buffer (7 μL), and end repair andT-tailing enzyme mix (3 μL). The reaction can be incubated at 20° C. for30 minutes and then increased to 65° C. for 30 minutes. H₂O (5 μL) canthen added to the reaction (50 μL) along with 2.5 μL of 20 μM adaptor(P312+P313), 2.5 μL of 20 μM adaptor (P314+P315), ligation buffer (30μL), and DNA ligase (10 μL). The reaction can then be incubated at roomtemperature for 15 minutes, followed by a reaction clean-up. SPRI beadscan then be added and the reaction can be eluted. The adaptor ligatedlibrary (10 μL) can be incubated with H₂O (40 L) and 2× Kappa HiFimaster mix (50 μL) and it can be subjected to PCR (98° C. for 45seconds; 5 cycles of 98° C. for 15 seconds, 60° C. for 30 seconds, and72° C. for 30 seconds; 72° C. for 1 minute; and kept at 4° C.). Thisprotocol can then be modified in order to increase the number of cycles(e.g., from 5 cycles to 25 cycles). The second adaptor ligation reactioncomprises of a similar protocol as the one described for the firstadaptor ligation reaction; the difference being that 5 μL of 20 μMadaptor (P320+P321) can be used instead of 2.5 μL of 20 μM adaptor(P312+P313) and 2.5 μL of 20 μM adaptor (P314+P315).

Sequences:

P312 ACACTCTTTCCCTACACGACGCT (SEQ ID NO: Right adaptor 28) P313/5Phos/GCGTCGTGTAGGGAAAGAGTGT (SEQ ID Right adaptor NO: 29) P314/5Phos/CACTCTTTCCCTACACGACGCT (SEQ ID Left adaptor NO: 30) P315AGCGTCGTGTAGGGAAAGAGTGT Left adaptorCACTCTTTCCCTACACGACGCT (SEQ ID NO: 31) P316 ACACTTTATGCTTCCGGCTCAmp pUC18 for 200 bp frag CACTCTTTCCCTACACGACGCT (SEQ ID NO: 32)with KpnI in middle P317 TAAGTTGGGTAACGCCAGG Amp pUC18 for 200 bp fragCACTCTTTCCCTACACGACGCT (SEQ ID NO: 33) with KpnI in middle P318ACACTCTTTCC CACTCTTTCCCTACACGACGCT Invasion primers (SEQ ID NO: 34) P319AGCGTCGTG CACTCTTTCCCTACACGACGCT Invasion primers (SEQ ID NO: 35) P320TTCCAATGATACGGCGACCACCGAUACUGUCA Outside adaptor-can use P5UAGCTAGCTCCTCACTCTTTCCCTACACGACGC primer USER compatibleT (SEQ ID NO: 36) P321 /5Phos/GGAGCTAGCTATGACAGTATCGGTGGTCOutside adaptor-can use P5 GCCGTATCATTACTT primerCACTCTTTCCCTACACGACGCT (SEQ ID NO: 37)

Example 5: Improved Conversion Efficiency (RNA Sample to Next-GenerationSequence (NGS) Library) after 3′-Phosphate, 2′-Phosphate and 2′,3′-Cyclic Phosphate Removal

Some of the proposed or demonstrated techniques of the presentdisclosure require free 3′-hydroxyl at the 3′-end of an RNA sample. Forexample, 3′-OH is required for RNA poly(A) tailing with a polymerase(e.g., poly-A polymerase), and/or for DNA poly-tailing with terminaldeoxynucleotidyl transferase (TdT), and/or for ligation. Endogenous RNAusually contains a 3′-hydroxyl or a 2′,3′-cyclic phosphate or a3′-phosphate. The 3′-hydroxyl can be a product of transcription, poly(A)tail synthesis, or enzymatic cleavage (enzymes with catalytic mechanismsimilar to RNase H). The 2′,3′-cyclic phosphate can be a product ofenzymatic cleavage (enzymes like RNase A) or spontaneous hydrolysis(non-enzymatic intramolecular transphosphorylation). For example, RNAcan be cleaved by intramolecular transesterification.

The 2′,3′-cyclic phosphate is very common due to natural RNAphosphodiester bond instability and can occur naturally (cell free RNAdegradation) or as a result of sample treatment or storage. RNA samplesbearing 2′,3′-cyclic phosphate or 3′-phosphate cannot be subsequentlypoly-tailed or ligated because the presence of a free 3′-hydroxyl groupis required for both. For this reason, RNA samples with 2′,3′-cyclicphosphate or 3′-phosphate can be treated with a phosphatase (e.g., T4polynucleotide kinase (PNK) enzyme) to generate a 3′-hydroxyl group.Other examples of phosphatases are disclosed in TABLE 1 below (UshatiDas and Stewart Shuman, Mechanism of RNA 2′,3′-cyclic phosphateendhealing by T4 polynucleotide kinase-phosphatase, Nucleic AcidsResearch, 2013, vol. 41, No. 1, 355-365).

TABLE 1 Comparison of RNA repair enzymes that heal 2′, 3′-cyclicphosphate ends. Enzyme Metal Product CPDase prod 3′-Pase 2′Pase T4 PnkpMg 3′-OH, 2′-OH 3′-PO4, 2′-OH Yes Yes CthPnkp Mn, Ni 3′-OH, 2′-OH 3′-OH,2′-PO4 Yes Yes Yeast & plant None 3′-OH, 2′-PO4 3′-OH, 2′-PO4 No No tRNAligase RtcB Mn 3′-PO4, 2′-OH 3′-PO4, 2′-OH No ?

T4 polynucleotide kinase (PNK) enzyme includes both kinase andphosphatase enzymatic activities. Thus, to optimize the T4 PNK, thekinase enzymatic activity can be removed by substituting at least one ofthe catalytically essential amino acids. This results in the phosphatasebeing the only enzymatic activity present. Removing the kinase activityhelps with subsequent reactions such as poly-A tailing using ATP forexample, because ATP is also a kinase substrate. Examples of cell freeRNA NGS library preparation protocols including de-phosphorylation aredisclosed herein. Also disclosed herein are comparison reactions (e.g.,reactions not treated with T4 PNK).

Additional potential benefits: the unique properties of the 3′end of RNAparticles depending on the type of process used to generate the RNAparticles, allow one to focus and/or manipulate the sequencing library.For example, if one does not wish to sequence RNA fragments generateddue to process degradation (e.g., incomplete RNA fragments bearing2′,3′-cyclic phosphate), one can avoid treating the sample with T4 PNK.In this way, the library will include full mRNAs and miRNAs(3′-hydroxyl).

Example 7: RNA Sample Fragmentation is Part of the NGS LibraryPreparation Workflow; Enzymatic and Nonenzymatic Methods

Major DNA sequencing technologies, such as illumina or ion torrent, arelimited in regards to sequencing read-length (meaning that a limitednumber of bases can be sequenced in each individual read). Bothtechnologies have a read range of up to about 100 bp-500 bp, making itimpractical to use a library that significantly exceeds this range. Cellfree RNA usually ranges from about 20 to 2000 bases, formalin-fixedparaffin-embedded (FFPE) RNA ranges from about 20 to 500 bases and mRNAis usually around 2000bases. For practical reasons, samples are usuallyfragmented, so effective library size is no more than 400 bp. Sampleloading library fragments longer than 1000 bp is very inefficientcompared to shorter fragments. Disclosed herein are two general methodsof RNA sample fragmentation; enzymatic and non-enzymatic. The enzymaticmethod can use enzymes with RNase activity (e.g., RNase A, RNase P,RNase H, RNase III, RNase T1, RNase T2, RNase U2, RNase Vi, RNase I,RNase L, RNase PhyM, RNase V, dicer, or argonaute). The non-enzymaticmethod disclosed herein takes advantage of the natural chemicalinstability of RNAs. RNA can undergo spontaneous non-enzymaticfragmentation as a result of internal transphosphorylation. Breaking ofphosphodiester bonds of RNA can be brought about by various conditions(e.g., metals, such as Mg, Mn, Pb, or polyamines, or cofactors, such asPVP or PEG). An increase in the transphosphorylation rate can beachieved, for example, with high pH or with high(er) temperature.Non-enzymatic hydrolysis preferentially happens in single strandedportions of RNA particles, preferentially between bases UA or CA. Theadvantages of using a non-enzymatic method includes: simplicity andreliability (independent of enzyme activity or shelf life), and the factthat the reaction can be conducted in conditions compatible with themajority of the subsequent steps. TABLE 2 below shows a workflow of botha fragmentation protocol and a no-fragmentation protocol. The librarieswere prepared using cell free RNA sample.

TABLE 2 Workflow No Fragmentation With Fragmentation Work STEP_1 RNAfragmentation by heat flow: treatment STEP_1 PNK Treatment STEP_2 PNKTreatment STEP_2 Poly Adenylation using Poly-A STEP_3 Poly Adenylationusing Poly-A Polymerase Polymerase STEP_3 Poly T Primer annealing STEP_4Poly T Primer annealing STEP_4 2D-RT & Tagging reaction STEP_5 2D-RT &Tagging reaction STEP_5 primer-adapter excess and non- STEP_6primer-adapter excess and non- specific priming product cleaningspecific priming product cleaning with Magnetic beads with with Magneticbeads with immobilized oligoA immobilized oligoA STEP_6 SPRI cleanupSTEP_7 SPRI cleanup STEP_7 Sample Index PCR STEP_8 Sample Index PCRSTEP_8 SPRI cleanup STEP_9 SPRI cleanup

In short, the no-fragmentation protocol can include 6.5 μL of H₂O, 2 μLof 10×T4 PNK buffer, 0.5 μL of 10×RNase inhibitor, 1 μL of 10 U/μL T4PNK enzyme, and 10 μL sample (e.g., cell free RNA sample). The reactioncan then be incubated at 37° C. for 20 minutes, 70° C. for 4 minutes,and then placed on ice. 3.25 μL of H₂O, 10 μL of 5×2D PNK buffer, 1.25μL of 10×RNase inhibitor, 7.5 μL of 10 mM ATP, and 1.25 μL of 5 U/L Ecoli PolyA Pol can then be added to the reaction. The reaction can beincubated at 16° C. for 5 minutes and can then be placed on ice. 0.5 μLof 100×dNTPs, 1 μL of 10 μM P334 Primer, 0.25 μL of 100 μM P423 DNA teracc can then be added to the reaction. The reaction can be incubated at70° C. for 2 minutes, and can then be placed on ice for 2 minutes. 1.25μL of 10×RNase inhibitor, 3.75 μL of P2 (e.g., R2 variant at 1 g/L canbe added to the reaction (for a total of 50 μL reaction). The reactioncan be incubated at 34° C. for 1 hour, pulled down, spri 1.6×, theneluted in 50 μL. In some instances, a reverse transcriptase or amodified reverse transcriptase, or an enzyme that has similar functionto a reverse transcriptase can be used instead of P2.

In short, the fragmentation protocol can include 1 μL of 10× buffer Aand 9 μL of sample (e.g., cell free RNA sample). The reaction can beincubated at 94° C. for 4 minutes and can then be placed on ice. 14.75μL of H₂O, 3 μL of 10× buffer B, 0.75 μL of 10×RNase inhibitor, and 1.5μL of 10 U/μL T4 PNK enzyme can be added to the reaction. The reactioncan be incubated at 37° C. for 30 minutes, at 72° C. for 3 minutes andcan then be placed on ice. 5 μL of 10× buffer C, 1.25 μL of 10×RNaseinhibitor, 7.5 μL of 10 mM ATP, and 1.25 μL of 5 U/L E coli PolyA Polcan then be added to the reaction. The reaction can be incubated at 16°C. for 5 minutes and can then be placed on ice. 0.5 μL of 100×dNTPs, 1μL of 10 μM P334 Primer, 0.25 μL of 100 μM P423 DNA ter acc can then beadded to the reaction. The reaction can be incubated at 70° C. for 2minutes, and can then be placed on ice for 2 minutes. 1.25 μL of10×RNase inhibitor and 3.75 μL of P2 (e.g., R2 variant at 1 g/L (e.g.,an R2 RT N-truncation, such as SEQ ID NO: 50)) (can be added to thereaction (for a total of 50 μL reaction). The reaction can be incubatedat 34° C. for 1 hour, pulled down, spri 1.6×, then eluted in 50 μL. Insome instances, a reverse transcriptase or a modified reversetranscriptase, or an enzyme that has similar function to a reversetranscriptase can be used instead of P2.

In short, the 5×2D PNK buffer can include 645 μL of H₂O, 10 μL of 1000mM Tris-HCl pH 7.5, 300 μL of 5000 mM NaCl₂, 5 μL of 1000 mM MgCl₂, 25μL of 10% tween, and 15 μL of 1000 mM DTT. The buffer A stock caninclude 60 μL of H₂O, 10 μL of 1000 mM Tris-HCl pH 8.3, and 30 μL of1000 mM MgCl₂. The buffer B stock can include 45 μL of H₂O, 50 μL of1000 mM Tris-HCl pH 7.5, and 5 μL of 1000 mM DTT. The buffer C stock caninclude 36 μL of H₂O, 60 μL of 5000 mM NaCl₂, 2.5 μL of 10% tween, and1.5 μL of 1000 mM DTT. The 10×PNK buffer can include 150 μL of H₂O, 700μL of 1000 mM Tris-HCl pH 7.5, 100 μL of MgCl₂, and 50 μL of 1000 mMDTT. The 100× balanced dNTPs can include 100 μL of H₂O, 75 μL of 100 mMdATP, 75 μL of 100 mM of dTTP, 375 μL of 100 mM dGTP, and 375 μL of 100mM dCTP. The 5×R2 buffer+dNTPs can include 430 μL of H₂O, 150 μL of 1000mM Tris-HCl pH 7.5, 300 μL of 5000 mM NaCl₂, 25 μL of 1000 mM MgCl₂, 25μL of 10% tween, 25 μL of 1000 mM DTT, 3.75 μL of 100 mM dATP, 3.75 μLof 100 mM of dTTP, 18.75 μL of 100 mM dGTP, and 18.75 μL of 100 mM dCTP.The streptavidin magnetic beads can include 160 μL of streptavidinmagnetic beads (NEB) saturated with biotinylated oligoAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA/3BioTEG/; beads can be resuspendedin 10 mM Tris pH7.5, 300 mM NaCl₂. The primer sequences used can be:P334 (A/iSp9/CCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT NNNNNNNNTTTTTTTTTTTTTTTTT) (SEQ ID NO: 93); P423(AA/iSp9/ACACTCTTTCCCTACACGACGCTCTTCCGATCT/3ddC/) (SEQ ID NO: 94); P399(AATGATACGGCGACCACCGAGATCTACACGTACTGACACACTCTTTCCCTACACGA CGC) (SEQ IDNO: 95); P400(CAAGCAGAAGACGGCATACGAGATATTACTCGGTGACTGGAGTTCAGACGTGT)(SEQ ID NO: 96)

Example 9: Robust Mechanism of R2 RT Jumping

R2 RT jumping is a very efficient mechanism. It is much less sensitiveto the acceptor-adapter sequences compared to template switchingmechanisms (e.g., methods that use MMLV). This low sensitivity allowsfor optimal utilization of sequencing adapters in the Illuminasequencing for example. In this experiment, a variety of acceptors canbe tested. This experiment can be used to show efficiency similaritiesbetween RNA and DNA acceptors. The use of DNA acceptors allow forcheaper and more reliable and/or stable technology. This experiment canbe used to show that the conversion efficiency is not sensitive to the3′-end of the acceptor sequences. Thus, this mechanism allows forflexibility regarding acceptor sequences and it is relevant for both RNAand DNA samples. Examples of acceptors used:

1) (SEQ ID NO: 80) AA/iSp9/ACACTCTTTCCCTACACGACGCTCTTCCGATCTAGGG/ 3ddC/;2) (SEQ ID NO: 81) AA/iSp9/ACACTCTTTCCCTACACGACGCTCTTCCGATCTCAGGG/3ddC/; 3) (SEQ ID NO: 82)AA/iSp9/ACACTCTTTCCCTACACGACGCTCTTCCGATCTTCTGGG/ 3ddC/; 4)(SEQ ID NO: 83) AA/iSp9/ACACTCTTTCCCTACACGACGCTCTTCCGATCTG/3ddC/; 5)(SEQ ID NO: 84) AA/iSp9/ACACTCTTTCCCTACACGACGCTCTTCCGATCT/3ddC/; 6)(SEQ ID NO: 85) AA/iSp9/ACACTCTTTCCCTACACGACGCTCTTCCGATCTrGrGrG/ 3ddC/;7) (SEQ ID NO: 86) AAAA/iSp9/ACACTCTTTCCCTACACGACGCTCTTCCGATCTrGrGr G;8) (SEQ ID NO: 87) AA/iSp9/ACACTCTTTCCCTACACGACGCTCTTCCGATCTN/3ddC/; 9)(SEQ ID NO: 88) AA/iSp9/ACACTCTTTCCCTACACGACGCTCTTCCGATCTNN/3ddC/; 10)(SEQ ID NO: 89) AA/iSp9/ACACTCTTTCCCTACACGACGCTCTTCCGATCT*/3ddC/; 11)(SEQ ID NO: 90) AA/iSp9/ACACTCTTTCCCTACACGACGCTCTTCCGATCTN/ideoxyI//3ddC/; 12) (SEQ ID NO: 91)AA/iSp9/ACACTCTTTCCCTACACGACGCTCTTCCGATC/iSuper- dT//3ddC/; and 13)(SEQ ID NO: 92) A/iSp9/CCGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT/ 3ddC/.

Example 10: Poly-A Tail Length Control, Method with Non-ExtendableNucleotide

PolyA polymerase is an RNA polymerase used frequently to generate apoly-A tail on the 3′ end of an RNA (e.g., poly-A polymerase form E.coli or yeast). Poly-A polymerase has enzymatic activity that allows forthe generation of an RNA chain (i.e., extension of the 3′end of an RNA)without an RNA or DNA template. Although, poly-A polymerase preferablysynthesizes a poly-A tail, poly-A polymerase also has activity withother ribonucleotides (e.g., CTP, GTP and UTP). Controlling the poly-Atail length is important for sequencing quality and yield. Typically,ATP concentration and reaction time and/or temperature are used tocontrol the poly-A tail length. Alternative methods can be used, such asusing a blocking (un-extendable) nucleotide (e.g.,3′-Deoxyadenosine-5′-Triphosphate (an ATP analog)). Once a blockingnucleotide, 3′-Deoxyadenosine-5′-Triphosphate, is incorporated to an RNAchain analog, it cannot be further extended due to a lack of a 3′hydroxyl group. Various concentrations of ATP and3′-Deoxyadenosine-5′-Triphosphate can be used. Poly-A tail length can becontrolled based on the concentration/ratio of ATP and3′-Deoxyadenosine-5′-Triphosphate, which is independent of reaction timeand/or enzyme concentration. This method provides for significantprotocol advantage when applied to high throughput or automatedprocesses.

Example 11: Library Preparation, Depletion of Ribosomal RNA (rRNA) andTransfer RNA (tRNA) to Maximize Sequencing Throughput

Approximately 80% of the total RNA in cells is rRNA and 15% is tRNA.Ribosomal RNA rarely serves as a diagnostic target. Therefore, becauseof that, the practice is to remove/deplete rRNA and tRNA from sequencinglibraries. The amount of rRNA and tRNA in sequencing libraries can becontrolled at various stages of library preparation. For example,depletion of rRNA and tRNA can occur during the early stages, e.g.,after total RNA isolation (RNA level), or after PCR amplification (dsDNAlevel). Two general methods to remove rRNA and tRNA is describedherein: 1) pulling rRNA/tRNA or PCR products using complementaryoligonucleotide attached to magnetic beads or solid support; and 2)oligonucleotide-guided degradation of the rRNA/tRNA or PCR products.

Method 1: In this method, amplified dsDNA can be denatured andhybridized to a pool of strategically designed oligonucleotides.Oligonucleotides are complementary to one or both DNA strands with rDNAsequence. For Illumina library, only one strand may be depleted as onlyone polarity is used in bridge amplification. Each oligonucleotideincludes biotin modification. Ribosomal sequences (including DNAfragments) can be depleted/removed using straptvidin-immobilizedmagnetic beads or solid support. In some cases, depletion can beperformed after PCR library amplification in order to mitigate losses ofrare and low represented sequences. Depletion can also be performedduring the early stages of library preparation (e.g., RNA level).

Example 12: A Method to Express the R2 Retrotransposon

Described herein are two methods of expressing the R2 retrotransposonenzyme: the first, involves the removal of the N-terminal domain, andthe second, involves tag-fusion stabilization.

Method 1: N-terminal domain removal. This method can be used totransform the R2 retrotransposon, while increasing its protection,leading to increase expression in E. Coli and improved stability. It isimportant to note, however, that due to its eukaryotic origin as well asthe structure and complexity of its R2 retroelements, a high level ofexpression, and thus, production is difficult to achieve. These R2retroelements are multi-domain elements with a molecular mass that isusually over 100 kD. These elements are composed of three major domains(see, FIG. 1C): (1) the N-terminal domain, which usually includes DNAbinding motifs zinc-finger and c-myb (see, FIG. 1A and FIG. 1 ). Thisdomain contributes to the ability of the R2 retrotransposon to havespecific recognition and to bind to target DNA through the target primedreverse transcription mechanism (TPRT); (2) reverse transcriptase, whichis responsible for copying the R2 RNA template; and (3) the endonucleasedomain, which is responsible for the specific cleavage of target DNA.

This method, based on the underlying principle that the presence of theN-terminal domain interferes with the expression and stability of the R2retroelement, focuses on the full or partial removal of the N-terminaldomain. The removal method can be focused on either the full N-terminaldomain, only a part of it, thus, a partial N-terminal domain removal.This method improves the expression and stability of the R2 proteinwithout negatively affecting the enzyme's performance in the downstreamprocess of library preparation (see, FIGS. 1A, B, and C).

Method 2: Tag-fusion stabilization. This method involves the extensionof Method 1, whereby the N-terminal domain is removed, in combinationwith fusion-tags. These tags include: Fh8, MBP, NusA, Trx, SUMO, GST,SET, GB1, ZZ, HaloTag, SNUT, Skp, T7PK, EspA, Mocr, Ecotin, CaBP, ArsC,IF2-domain I, an expressivity tag, an expressivity tag that is part ofIF2-domain I, RpoA, SlyD, Tsf, RpoS, PotD, Crr, msyB, yjgD, rpoD, His6,His-tag, His6-tag, Calmodulin-tag, CBP, CYD (covalent yet dissociableNorpD peptide), Strep II, FLAG-tag, HA-tag, Myc-tag, S-tag, SBP-tag,Softag-1, Softag-3, V5-tag, Xpress-tag, Isopeptag, SpyTag, B, HPC (heavychain of protein C) peptide tags, GST, MBP, biotin, biotin carboxylcarrier protein, glutathione-S-transferase-tag, green fluorescentprotein-tag, maltose binding protein-tag, Nus-tag, Strep-tag, andthioredoxin-tag.

Example 13: Mutagenesis of R2 Retrotransposon Motif-1, Motif 0, andThumb Domain

Mutagenesis of motif-1 and motif 0. The reverse transcriptases (RTs)that are the most studied and best described in the literature are thoseof retroviral and long terminal repeats (LTR)-retrotransposon origin.This family of reverse transcriptases shares seven highly conservativeamino acid sequence motifs. RTs encoded by non-LTR retroelements as wellas those encoded by telomerases include additional conservative motifslocated at the N-terminal of the RT. These are referred to in theliterature as motif-1 and motif-0. It was hypothesized that the non-LTRretroelement motifs-1 and 0 retain functional similarity to telomerasemotif CP and T (part of RNA-Binding Domain (TRBD), see FIG. 3 ). Somereports also demonstrate the involvement of motif-1 and motif 0 ininteractions with specific R2 RNA templates as well as other templates,contributing to the R2 jumping mechanism. This method focuses on themutagenesis of motif-1 and motif 0 (see, FIG. 2 ). This mutagenesisresults in an increase in jumping efficiency, single-stranded primingefficiency and processivity, as well as a significant reduction in biastoward RNA with similar sequences.

Mutagenesis of thumb domain. The thumb domain is mostly responsible forholding and/or interacting with the primer or the primer/template. R2RTs possess a unique capability to use a single-stranded primer comparedto other retroviral enzymes. More specifically, using defined sequencesof single-stranded DNA primer, R2 RTs can prime the reversetranscription at the 3′-end of random RNA templates. This reaction doesnot require base pairing with the RNA template (see, FIG. 10 ). Thisproperty of R2 is perhaps linked to Target Primed Reverse Transcription(TPRT). In this mechanism, the R2 retrotransposon recognizes a specificdouble stranded DNA (dsDNA) sequence than endonuclease domain of R2 andcleaves one of the strands. The cleaved strand can then be transferredto the RT catalytic center and the 3′-end of the strand can be used as aprimer. In this method, the R2 thumb domain can be mutagenized toimprove single-stranded priming efficiency and processivity (see, FIG. 4).

Example 14: Method to Prepare RNA Library for Single Cell and Low InputSamples

Methods for single cell library preparation include, but are not limitedto, confinement techniques focused on emulsion and nanofabrication.Other methods include cell sorting and serial dilution. Librarypreparation involving single cells and/or low RNA sample inputs (5-50μg) have many challenges, and as such, limitations. Due to the smallsample size, the possible presence of artifacts, and the presence ofexcess reaction reagents like oligo adapters and primers (in this case,outnumbering the RNA sample), one of the many challenges is the risk ofartifact amplification. To ensure high quality library preparation, twomajor conditions must be met: the first being high conversionefficiency, thus, input RNA to DNA library, and the second, is a lowoligo adapter-adapter product. The enzymatic platform of the presentdisclosure provides the possibility to use a simple technique thatresults in the necessary high RNA-sample-library conversion efficiencywhile ensuring relatively small sample loss. This small sample loss ismainly due to the shorter protocol, hence, less number of total steps inthe method. Unlike current methods, which are limited to targetPoly-adenylated RNA from the cells, the method described in the presentdisclosure can also capture non-polyadenylated RNA, like miRNA, andncRNA lincRNA.

Example 15: Method to Anneal rRNA Fragments Using DNA-Sponge

A large majority of the RNA in cells consists of ribosomal RNA (rRNA),whereby 80% of the cell's RNA is rRNA. Another 15% consists of transferRNA (tRNA) and other translational RNA machinery. Various methods havebeen developed to deplete rRNA and tRNA. These methods are based on twogeneral ideas: the first, pulling rRNA using specific oligonucleotideprobes attached to solid support, and the second, a specific probeguided degradation of the rRNA sequences, which is usually enzymatic.This depletion can be executed before library preparation, at the RNAlevel, or after library preparation, at the dsDNA level. In most currentapproaches, however, rRNA sequence depletion is an entirely separate anddistinct protocol, thus, adding to the process of sample preparation.

In this method, rRNA sequence depletion can be integrated into theprocess of sample preparation. Briefly, during or right after RNA samplefragmentation ssDNA that is complementary to rRNA, referred to as theDNA-sponge, can be included in the library preparation reaction. TheDNA-sponge consists of complete or large DNA fragments coveringsequences of rRNA subunits. The length of the DNA-sponge is a multiplexof the length of average RNA sample after the fragmentation and can havea linear form with blocked 3′end, or a circular form, or it can beconcatemerized. The main function of the DNA-sponge is to anneal to rRNAfragments. The annealing of the rRNA fragments to large complementaryssDNA make the 3′-end of the rRNA fragment not available to poly Apolymerase (in a method with polyA tailing) or to 3′-priming by R2enzyme (method with random 3′-end priming with ssDNA adapter). As such,rRNA fragments with no available 3′-end are not converted to thesequencing library (see, FIG. 5 and FIG. 6 ).

Example 16: Direct RNA and ssDNA Sequencing with R2 Enzyme

The non-naturally occurring R2 reverse transcriptase (RT) of the presentdisclosure can be used directly for RNA or ssDNA sequencing focused onsingle-molecule sequencing technology whereby confinement methods can beoptic, microscopy-based, nanopore-based or field-effecttransistors-based.

In this method, the R2 enzyme can be used as a tool for direct RNAsequencing using single-molecule technology, which as described abovecan be optic, microscopy-based, nanopore-based or field-effecttransistors-based. These single-molecule sequencing methods require aprocessive enzyme since the essential property of these techniques isthe enzyme/protein processivity. Direct RNA sequencing can be conductedwith either Reverse transcriptase (RT) or RNA-directed-RNA polymerase.RTs of retroviral origin may be low processivity polymerases withpolymerase-template complex lifetime of ˜30 s. The R2-template complex,on the other hand, has a lifetime that is in the range of ˜30 min. Inthis method, this enzyme can be used for direct RNA sequencing. Thedirect sequencing has a main advantage, which is that there is no needfor conversion to DNA and the additional possibilities to detect RNAmodifications, such as methylation.

Example 17: R2 Based Method for In Situ RNAseq

RNA-sequencing profiles gene expression over the whole transcriptome,but it lacks spatial context. In situ RNAseq allowed genome-wideprofiling of gene expression in situ in fixed cells and tissues (see,FIG. 6 ). These cells and tissues can be from any animal which maybenefit from the methods of the disclosure, including, e.g., humans andnon-human mammals, such as primates, rodents, horses, dogs and cats.Subjects include without limitation a eukaryotic organism, a mammal suchas a primate, e.g., chimpanzee or human, cow; dog; cat; a rodent, e.g.,guinea pig, rat, mouse; rabbit; or a bird; reptile; or fish. Subjectsspecifically intended for treatment using the methods described hereininclude humans. A subject may be an individual or a patient.

In this method, RNA from fixed cells and/or tissues can be convertedinto cDNA and directly sequenced using single-molecule methods or bytagging the with barcode information including spatial-information. ThiscDNA can then be converted to sequencing library. One of the methods ofspatial-specific barcoding can be by using a glass plate with printed inspatial-specific manner oligonucleotide primer (FIG. 6 ). The cDNA isgenerated using a slice of tissue.

In the methods of the present disclosure, the non-naturally occurring R2enzyme and the jumping method can be used for spatial specific librarygeneration. The primer can be specifically barcoded with poly Toligonucleotides (see, FIG. 6 ) and applied modification of the poly Abased library preparation protocol. This method is highly efficient andthe high conversion efficiency is critical for this application. Due tothe nature of the samples (single cells, small tissue, etc), this methodneeds to be very sensitive and thus, operate with very low sample input.For this method, either a specific primer or a random primer can beused.

Example 18: RNA-Sequencing Library Preparation: A Poly-A-Based Methodfor Total-RNA, mRNA, miRNA, and cfRNA

The methods described below require a poly A tail at the 3′-end of theRNA sample. A natural poly A can be used for the mRNA protocol. For theprotocols for total-RNA, miRNA, and cfRNA, the poly A that is used canbe synthesized with poly A polymerase or alternatively, poly Upolymerase. Depending on which sequencing technology is used aftersample preparation (either a long-read or short-read); RNA samplefragmentation can also be applied.

General Poly-A based method. In a first step, the RNA sample can befragmented. Several methods for fragmentation can be used, including butnot limited to spontaneous RNA-magnesium-induced degradation orenzymatic cleavage (see, FIG. 7 ). Depending on the fragmentation methodthat is used, the cleavage may generate 3′-OH or cyclic 2′,3′-phosphateat the 3′-end of the RNA fragment. For example, the method withspontaneous magnesium-catalyzed hydrolysis can produce 2′, 3′-phosphate,which needs to be removed in order to generate 3′ poly A tail with polyA polymerase. To remove the phosphate from the 3′-end, an enzymaticreaction where T4 polynucleotide kinase (PNK) is applied. It isimportant to note that T4 PNK includes two enzymatic activities: 5′kinase and cyclic 2′,3′-phosphatase. After de-phosphorylation, the PNKcan be temperature inactivated and RNA 3′-end can be poly A tailed withpoly-A polymerase or alternatively, poly-U polymerase. Following thepoly A polymerase temperature inactivation, poly A tailed RNA can bemixed with primer-adapter, including oligo-T sequences,acceptor-adapter, and R2 enzyme. Annealed to RNA poly-A tail oligo-Tadapter can be used as a primer in an extension reaction catalyzed by R2enzyme (reverse transcription). After reaching the 5′end of the RNAtemplate, the R2 extension complex jumps to the 3′-end of theacceptor-adapter, and continues the extension. Extension can then bepaused on the nucleotide analog, also referred to as the blocker, whichis strategically incorporated in the adapter toward the 5′-end of theadapter. Blocking the analog prevent the R2 extension complex fromsecond jumping (both primer-adapter and acceptor-adapter includesblocker nucleotide, blocker nucleotide analog here is Spacer 9). Duringthe reaction, artifacts can be generated includingprimer-adapter-acceptor-adapter dimers or homogenous dimers (see, FIG. 9). The adapter dimers artifacts including acceptor extension areprevented by 3′-dideoxy nucleotide at the acceptor-adapter 3′-end.Alternatively, different extension blockers can be applied, such as3′phospho-dNTP, 3′amino-dNTP. The artifacts primed by primer-adapter,including poly-T sequence, can be removed from the reaction with oligo-Aattached to magnetic beads. The artifacts can be primed withoutannealing (template primer duplex formation) so the primer sequenceremains single-stranded (see, FIG. 9 ). After pulling with oligo-Aimmobilized magnetic beads, additional cleanup with solid phase reverseimmobilization (SPRI) can be conducted. The last step is polymerasechain reaction (PCR) amplification using primers that are complementaryto both the primer- and the acceptor-adapter. The primers may includeadditional sequences for additional applications, such as barcodes, oradapter sequences that are compatible with/recommended by majorsequencing technologies, such as Illumina, Ion Torrent, and PacBio, andRoche 454.

Shorter poly-A based method. In this method, engineered T4 PNK can beused. The modified enzyme retains only one enzymatic activity cyclic2′,3′-phosphatase and kinase activity can be removed. This change canallow the simultaneous use of both enzymes T4 PNK and poly-A polymerasewithout breaking the protocol into two separate steps. Both enzymes usethe same substrate, ATP. As such, PNK mutation can be used to preventthe depletion of ATP and the 5′-end phosphorylation of the sample.

In a first step, the RNA sample can be fragmented (for long readsequencing; miRNA application fragmentation is not required). Dependingon the method that is used, cleavage may generate 3′-OH or cyclic2′,3′-phosphate at the 3′-end of the RNA fragment. To remove phosphatefrom 3′-end, enzymatic de-phosphorylation with T4 polynucleotide kinasecan be applied (engineered T4 PNK—only cyclic 2′,3′-phasphataseactivity). De-phosphorylation can be conducted simultaneously withsample RNA 3′-end poly-A tailing with poly-A polymerase, oralternatively poly-U polymerase. After a short incubation, the reactioncan be stopped by temperature inactivation. All subsequent steps are thesame as the ones for the general poly-A based method described above.

TABLE 3 Protocol for Total RNA Library Prep: Total RNA [stock] Reagentvol [final] PNK MM H2O  0  10 X T4 PNK buffer  2 1  10 X Rnase Inhibitor 0.5 0.25  10 U/ul T4 PNK enz  1 0.5 Sample 16.5 0 Total 20 37 C., 20′-- > 70 C., 4′ -- > on Ice Poly A Pol H2O  8.5 MM  5 X 2D PNK buffer 101  10 X Rnase Inhibitor  1.25 0.25  10 mM ATP  2 0.4  5 U/uL Ecoli PolyAPol  1.25 0.125 16 C. for 5 mins and then move to ice P/A MM H2O  1.15100 X dNTPs  0.5 1 100 uM P334 Primer  0.1 0.2 100 uM P423 DNA ter acc 0.25 0.5 Incubate at 70 C., 2 mins -- > On ice for 2′ Enz MM  10 XRnase Inhibitor  1.25 0.25  40 P2 enzyme (1 mg/mL)  3.75 3 Total 50 34C., 1 hr -- > Pull down -- > spri 1.6x -- > Elute in 50 uL Pull downwith pre-prepared beads 30 mins Before PCR cleanup SPRI 80 ul Elution 25uL [stock] Reagent vol [final] Thermocycling 2D H2O 0 0 95 c-3 minLibrary  2 x Kapa Hifi MM 25 1 98 c-20 sec 14 amp PCR 10 uM SI primerP5 + P7 1.25 0.25 61 c-15 sec cycles Template 23.75 0 72 c-20 sec Total50 72 c-1 min 4-forever Post PCR cleanup SPRI 60 ul Elution 25 uL

TABLE 4 Protocol for miRNA Library Prep: miRNA Template [stock] Reagentvol [final] PolyA rxn H2O  0.00 H2O 11.2 10 X Poly(A) Pol Rxn  2 1Buffer 10 X Rnase Inhibitor  0.5 0.25 10 mM ATP  0.8 0.4  5 U/uL EcoliPoly A Pol  0.5 0.125 Sample  5 Total 20 32 C. for 20 mins and then moveto ice dNTP/P/A  5 X 2D miRNA buffer  4 0.4 dNTP/Accep/Primer  2 MixIncubate at 70 C., 2 mins -- > On ice for 2′ Enz 10 X Rnase Inhibitor 1.25 0.25 40 P2 enzyme (1 mg/mL)  3.75 3 Total 50 34 C., 1 hr -- > Pulldown Pull down with pre-prepared beads 30 mins Before PCR cleanup SPRI80 ul Elution 25 uL [stock] Reagent vol [final] 2D H2O  0 0 12 cyclesLibrary  2 x Kapa Hifi MM 25 1 amp 10 uM SI primer P5 + P7  1.25 0.25PCR Template 23.75 0 Total 50 Post PCR cleanup SPRI 60 ul Elution 25 uL[stock] [final] 5X miRNA Buffer Vol (uL) H2O  695 1000 50 mM Tris-HC1 50 pH7.5 5000 1000 mM NaCl2  200 1000 5 mM MgCl2   5  10 0.25 % Tween 25 1000 25 mM DTT  25 Total 1000 dNTP/Accep/Primer Mix [stock] vol (uL)[final] H2O 1.15 100 X dNTPs 0.5  1 100 uM P334 Primer 0.1  0.2 100 uMP423 DNA ter acc 0.25 0.5 Total    2 uL/rxn

TABLE 5 Protocol for mRNA temp ng 10 1 [stock] Reagent Vol [final] H2O15.25 5 X 2D buffer + dNTPs 10 1 10 X Rnase Inhibitor 1.25 0.25 10 uMP334 Primer 1 0.2 10 uM P423 terminated acceptor 2.5 0.5 5 ng/uL 15TotalHumanBrainRNA + ERCC Incubate at Temperature, varying mins --> Onice for 2′ 10 X Rnase Inhibitor 1.25 0.25 40 P2 enzyme (1 mg/mL) 3.75 3Total 50 34 C., 30 min --> spri 0.8x

TABLE 6 Protocol for 2D library amplification PCR Library amp PCRThermocycling [stock] Reagent Vol [final] 95 c.-3 min H2O 0 0 98 c.-20sec 15 2 x Kapa Hifi MM 50 1 61 c.-15 sec cycles 10 uM SI primer P5 + P72.5 0.25 72 c.-20 sec Template 47.5 0 72 c.-1 min Total 100 4-foreverCleanup SPRI 1.2X 5X R2 Buffer + vol [stock] [final] dNTPs (uL) H2O 4301000  150 mM Tris- 150 HCl pH 7.5 5000  1500 mM 300 NaCl2 1000  25 mM 25MgCl2  10 0.25 % Tween 25 100 0.375 mM dATP 3.75 100 0.375 mM dTTP 3.75100 1.875 mM dGTP 18.75 100 1.875 mM dCTP 18.75 1000  25 mM DTT 25 Total1000

Example 19: RNA-Sequencing Library Preparation: A Method Using RandomFragmentation for Total-RNA, mRNA, miRNA, and cfRNA

This method focuses on random priming using the random fragmentation ofthe RNA samples in combination with the unique properties of the R2enzyme. Here, the R2 enzyme is capable of priming the extension reactionwithout template-primer annealing. In this mechanism, extension can beprimed on the 3′-end of the template by a ssDNA primer without acomplementary sequence annealing to the template strand (R2 3′-endpriming, see, FIG. 10 ). In contrast to random priming with a randomoligonucleotide primer, the R2 3′-end priming efficiency is lesstemplate-length dependent and as such, library products are a fulllength copy of the template strand.

In a first step, the RNA sample can be fragmented. Here, severalfragmentation methods can be used for this first step, including but notlimited to spontaneous RNA hydrolysis with magnesium, or enzymaticcleavage (see, FIG. 11 ). After this first fragmentation step, the RNAsample can be mixed with primer-adapter (ssDNA), R2 enzyme, andacceptor-adapter (ssDNA or RNA). With dNTP present, the R2 enzyme canprime the extension at the template RNA 3′-end using ssDNAprimer-adapter. Once the extension reaches the 5′end of the RNAtemplate, the R2 enzyme can jump to the acceptor-adapter and cancontinue the reaction, pausing on the nucleotide analog, or blocker,which is strategically incorporated to the adapter toward the 5′-end ofthe adapter. The blocker nucleotide analog here is Spacer 9. Theblocking of the analog prevents the R2 extension complex from a secondjumping mechanism (both primer-adapter and acceptor-adapter includeblocker nucleotide). In the next step, the reaction can be cleaned withsolid phase reverse immobilization (SPRI). Similarly, size selection canbe used to remove some adapter-adapter dimer artifacts. The last step ispolymerase chain reaction (PCR) amplification whereby primerscomplementary to both the primer- and the acceptor-adapter can be used.These primers may include additional sequences for applications such asbarcoding and/or adapter sequences that are compatible with/recommendedby major sequencing technologies, such as Illumina, Ion Torrent, PacBio,and Roche 454.

TABLE 7 Protocol for miRNA Random libraries [stock] Reagent vol [final]H2O 14.7 5 X 2D nmer frag buffer 4 1 100 uM nMer Primer P591 0.1 0.5 100ng/ul Total HumanBrain 1.25 RNA Total 20 Incubate at 94 C., 3 mins -->On ice for 2′ H2O 12 5 X 2d nmer buff2 10 1 10 X Rnase Inhibitor 1.250.25 40 P2 enzyme (1 mg/mL) 3.75 3 Incubate at RT, 5 mins 100 X dNTPs0.5 1 10 uM P423 DNA ter acc 2.5 0.5 Total 50 30 C., 60 min --> spri0.7x (x2) --> Elute in 50 uL [stock] Reagent Vol [final] ThermocyclingH2O 0 0 95 c.-3 min 15 2 x Kapa Hifi MM 25 1 98 c.-20 sec cycles 10 uMSI primer P5 + P7 2.5 0.5 61 c.-15 sec Template 22.5 0 72 c.-20 secTotal 50 72 c.-1 min 4-forever 5X 2D nmer frag vol [stock] [final]buffer (uL) H2O 875 1000 100 mM Tris-HCl pH 8.5 100 5000 0 mM NaCl2 01000 25 mM MgCl2 25 10 0 % Tween 0 1000 0 mM DTT 0 Total 1000 vol[stock] [final] 5X 2d nmer buff2 (uL) H2O 765 1000 110 mM Tris-HCl pH7.5 110 5000 300 mM NaCl2 60 1000 15 mM MgCl2 15 10 0.25 % Tween 25 100025 mM DTT 25 Total 1000

Example 20: Method for Abundant RNA Depletion from Full Length andFragmented Sample Using Streptavidin-Magnetic-Beads to Remove RNAComprising Biotin-Labeled Primers

About 80% of the total RNA in cell is composed of ribosomal RNA (rRNA),another 15% is a transfer RNA (tRNA) and other translation RNAmachinery. This example describes a method for depletion of abundantribosomal sequent subsequent to cDNA synthesis and incorporation of both3′- and 5′ sequencing adapters.

In this method, cDNA comprising sequencing adapters is firstpre-amplified with few PCR cycles, such as 1 single PCR cycle, but insome instances less than 10 or less than 5 PCR cycles using primerscomplementary to the adapter sequence. After the aforementionedpre-amplification step, the sample is mixed with strategically designedprobes complementary to ribosomal sequence (both PCR product polarity)and subjected to single cycle PCR.

The primers include nucleotide modification that allow for thebinding/immobilization to a solid support, such as a primer comprising abiotin modification that allows for the binding to a streptavidin solidsupport. After the aforementioned PCR cycles the cDNA product thatincorporated the primer is allowed to bind to the solid support and isthus removed from the liquid phase of the reaction. This product issubsequently removed from the reaction using magnetic beads coated withstreptavidin. See FIG. 21 .

Example 21: Method for Abundant RNA Depletion from Full Length andFragmented Sample Using 5′-End Protected Oligo (PCR Primer)

About 80% of the total RNA in cell is composed of ribosomal RNA (rRNA),another 15% is a transfer RNA (tRNA) and other translation RNAmachinery. This example describes a method for the depletion of abundantribosomal sequent after cDNA synthesis and incorporation of both 3′- and5′ modified sequencing adapters (See FIG. 22 ). These modified adaptershave a modification at their 5′-end that prevents enzymatic degradationby an 5′-to3′-exonuclease.

In this method a cDNA product including 3′- and 5′ partial sequenceadapters is subjected to PCR amplification using oligo primers where oneof the primers include nucleotide modification(s) at the 5′-endpreventing enzymatic degradation by 5′-to3′-exonuclease, such as lambdaexonuclease. These modified primers may be selected to have the samepolarity as the RNA strands that they are designed to hybridize.Alternatively, the primers may be designed to have the oppositepolarity.

After amplification the PCR product is digested with5′-to-3′-exonuclease. During enzymatic digestion, the unprotectedstrand(s) is/are removed from the PCR product, and only ssDNA PCRproduct with one particular polarity is retained. Subsequently, rRNAdepletion can be used by using, for instance, a commercial kit such asLexoGen RiboCop.

Example 22: Method for Enrichment and Deep Sequencing of the SelectedSingle Cell Libraries Using a Barcode as a Selective Target for PCRAmplification

This example describes the preparation of RNA-seq library(ies) from amultiplicity of single cells (single cell library) where each uniquesingle cell is individually barcoded. Each unique barcode is configuredto serve as a template for a specific PCR primer. The barcode design isto optimize for PCR specificity with individual specific primers. (SeeFIG. 23 ).

This library can be subsequently sequenced with moderate or lowsequencing deepness (number of reads per cell). Based on complete orpartial results from the sequencing, a single cell of interest may beselected from the single cell library. The barcode associated with suchsingle cells can be identified. These barcodes may then be used toenrich and amplify a pool of nucleic acids derived from a selectedsingle cell.

Example 23: Method for Direct RNA-Seq Library Preparation fromTissue/Cells Biomass without RNA Purification Step

This example describes the preparation of nucleic acid libraries fromtissue/cell biomass without RNA purification. Briefly, natural tissue ishomogenized in a master mix that is insensitive to cell componentsinhibition. The mix includes collagenasis, estalases and otherenzymes/protein promoting cell/tissue lysis, also a component libraryprep and reagents for converting RNA to RNA-seq library, including oneor more enzymes described herein. Because the R2 derived enzymesdescribed herein are resistant to the homogenizing reagents, the RNA-seqlibrary preparation can proceed without RNA purification step. The celldissociation and lysis reagents may include enzymes from a group ofCollagenase, Hyaluronidase, DNase, Elastase, Papain, protease Type XIV,Trypsin, Lipase, alpha-hemolysin, and detergents.

After lysis anyone of the protocols described above can be used for cDNAsynthesis. (See FIG. 24 ).

Example 24: Method for Direct RNA-Seq Library Preparation fromTissue/Cells Biomass without RNA Purification Step

This example describes the preparation of nucleic acid libraries fromtissue/cell biomass without RNA purification by selecting a small of thetissue with a selected morphology or a different sub-substructure of thetissue. The selected tissue may be then collected separately or it maybe collected together with a larger biopsy fragment. In this example,the selected tissue is labeled with a unique barcode on the adapter thatmay be used to retain the spatial information of the nucleic acids beinganalyzed, alternatively post library lysis/library prep mix can becollected by allowing the tissue slice to interact with surface (solidsupport) with immobilized oligonucleotide primer/adapter, where thisprimer-adapter is labeled to preserve the spatial information.

While preferred embodiments of the present invention have been shown anddescribed herein, it will be obvious to those skilled in the art thatsuch embodiments are provided by way of example only. It is not intendedthat the invention be limited by the specific examples provided withinthe specification. While the invention has been described with referenceto the aforementioned specification, the descriptions and illustrationsof the embodiments herein are not meant to be construed in a limitingsense. Numerous variations, changes, and substitutions will now occur tothose skilled in the art without departing from the invention.Furthermore, it shall be understood that all aspects of the inventionare not limited to the specific depictions, configurations or relativeproportions set forth herein which depend upon a variety of conditionsand variables. It should be understood that various alternatives to theembodiments of the invention described herein may be employed inpracticing the invention. It is therefore contemplated that theinvention shall also cover any such alternatives, modifications,variations or equivalents. It is intended that the following claimsdefine the scope of the invention and that methods and structures withinthe scope of these claims and their equivalents be covered thereby.

Example 25: Total RNA

Library preparation was performed by bringing sample volume up to 18 uL,adding 2 μl of nA (see Table 8) and mixing. The sample was fragmented,incubated at 94° C. for 6 minutes and placed on ice for 2 minutes. 25 μLof nB (see Table 8) was added and mixed followed by 5 μL of nC (seeTable 8) with mixing. The sample was incubated at 30° C. for 1 hour andstored at 4° C.

A 0.7×SPRI cleanup standard protocol was performed. A double SPRIcleanup can be performed in cases of low sample input. The sample waseluted in 24 μL EB and transferred to new PCR tubes (22.5 μL).

A sample index PCR was performed (see Table 10) by adding 25 μL of ‘Amp’mix to the cleaned sample. 2.5 μL of SI primer mix was added and mixedwell. A PCR thermocycler program was run with the following protocol:95° C. for 3 minutes; followed by n-cycles (dependent on input amount)of 98° C. for 20 seconds, 61° C. for 15 seconds, and 72° C. for 20seconds; followed by 72° C. for 1 minute.

Another 0.7×SPRI cleanup was performed using standard protocols. Thesample was then eluted in 20 μL EB and 18.5 μL transferred into new PCRtubes.

Library QC and sequencing were performed.

TABLE 8 Materials and Reaction Compositions 1 [stock] Reagent volTemplate 18 10 X Fragmentation Buffer 2 Tube nA Total 20 Incubate at 94C., 4 mins --> On ice, 2′ H2O 14.15 Tube nB 5 X 2d nmer buff2 10 100 uMnMer Primer P591 0.1 100 X dNTPs 0.5 100 uM P423 DNA ter acc 0.25 X 10 XRnase Inhibitor 1.25 Tube nC 40 R2 Enzyme (R2 Reverse 3.75transcriptase) Total 50 Incubate at 30 C. for 60 mins --> spri 0.7x -->Elute in 24 uL

TABLE 9 Materials and Reaction Compositions 2 5X 2d nmer vol [stock]buff2 (uL) H2O 885 1000 mM Tris-HCl pH 7.5 10 5000 mM NaCl2 60 1000 mMMgCl2 5 10 % Tween 25 1000 mM DTT 15 Total 1000

The 10× Fragmentation Buffer was made up of 9700 mM Tris-HC, 10 mMMgCl₂, and 50 mM DTT at a pH of 7.6.

TABLE 10 Sample Index PCR [stock] Reagent vol 95 c.-3 min H2O 0 98 c.-20sec cycle 2 x Kapa Hifi MM 25 Tube Amp 61 c.-15 sec 10 uM SI primer P5 +P7 2.5 72 c.-20 sec Template 22.5 72 c.-1 min Total 50 4-forever

The oligo primers used in the PCR were:

P423 (SEQ ID NO: 76) AA/iSp9/ACACTCTTTCCCTACACGACGCTCTTCCGATCT/3ddC/P591 (SEQ ID NO: 77) /5Sp9/GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTSample Index P5 Primers: P551 (SEQ ID NO: 78)AATGATACGGCGACCACCGAGATCTACACTAATCTTAACACTCTTTCCC TACA CGASample Index P7 Primers: P559 (SEQ ID NO: 79)CAAGCAGAAGACGGCATACGAGATATTACTCGGTGACTGGAGTTCAGAC G

Bioanalyzer traces of the fragmentation are shown in FIG. 25 and thelibrary molecule structure is illustrated in FIG. 26 .

The sequencing results, using Illumina hiseq, are shown in Table 11. Inthe experiment with rRNA depletion before sample preparation, the samplewas rRNA depleted using NEB Next rRNA Depletion (accordingly to NEBprotocol). The sequencing results showed good RNA-seq library qualityincluding percentage of the aligned reads, number of genes and coverageCV as shown in Table 11.

TABLE 11 Sequencing Data RNA Ribo RNA % % % % Template Depletion # ofreads RL input aligned abundant unaligned IG Human None 22056690 2 × 100100 ng 93 9 7 4 Brain mRNA Universal NEBNext 27949188 2 × 100 200 ng 929 8 4 Human rRNA Reference Depletion # of genes RNA Ribo (0.1 Coverage %% % Template Depletion FPKM) CV stranded Exons Intron Human None 226810.58 99 51 49 Brain mRNA Universal NEBNext 23237 0.58 99.3 51 45 HumanrRNA Reference Depletion

Example 26: Ribo Depletion Exemplary Protocol

A template was prepared by starting with 5 ng of library material,diluting the 5 ng of library material in a total of 10 μL of volumeusing 10 mM Tris pH 8.0. The diluted library material was transferred toa PCR tube for PCR.

A 1 cycle PCR was performed for pull down. To the 10 μL of library (5ng), 1.5 μL of Ribo depletion Primer Mix (stock concentration of 25 uM)was added. To that, 13.5 uL of 2× Kapa Hifi Mastermix was added. Thereaction was kept on ice during setup. The reaction was then placed on athermocycler and the following thermocycling protocol was run: 98° C.—1min- ->62° C.—2 mins-→72° C.—2 mins- -→1 cycle- -→hold at 20° C.

Pull Down Bead Preparation:

During the above PCR protocol, the pull down beads were prepared infollowing way. Ribo depletion pull down beads were vortexed to uniformlysuspend. 50p for each reaction was transferred into separate PCR tubes.The PCR tubes were spun down briefly and placed on a magnetic rack untilthe 1 cycle PCR was done. Once the PCR was done, the buffer was removedfrom the beads and discarded. 25 μL of the PCR reaction product wasadded to the beads and vortexed to mix and incubated at room temperatefor 15 minutes with mixing every 5 minutes. After 15 minutes the tubeswere transferred to the magnetic rack and the solution was allowed toclear. Once the solution was clear, 23 μL of it was transferred to afresh PCR tube and the amplification reaction was set up.

Sample index PCR was performed using the following protocol: Thereaction was placed on a thermocycler and the following thermocyclingprotocol was run:

-   -   Step 1: 98° C.—1 min    -   Step 2: 98° C.—20 sec    -   Step 3: 61° C.—15 sec    -   Step 4: 72° C.—20 sec    -   Step 5: Repeat Step 2-Step 4 for 6 cycles    -   Step 6: 72° C.—2 min    -   Step 7: 4° C.—HOLD

PCR cleanup was then performed (0.8×SPRI cleanup using Ampure beads).The library was eluted in 20 μL EB and 18 μL of the library wastransferred for storage, QC, and sequencing. The exemplary RiboDepletionProtocol is also shown in Table 12 and the bead washing protocol used isshown in Table 13. The wash buffer and resuspension buffer compositionsare shown in Tables 14 and 15 respectively.

TABLE 12 RiboDepletion Protocol Set up Biotin (18S) PCR [stock] reagentvol (uL) [final] H2O 0 2 x KapaHifi MM 13.5 1.08 25 uM Primers BiotinMix 1.5 1.5 Template 10 Total 25 Do 1 PCR cycle Pull down with stepbeads - 50 uL ready beads Final PCR h2o 32 2 x Kapa Hifi MM 40 0.8 10uMP5-P7 5 0.5 Template 23 Total 100 Do 6 PCR cycle 0.8x SPRI cleanup -->20 ul Elute

TABLE 13 Bead Washing Protocol Step Bead washing protocol 1 NEBstreptavedin beads 2 1 ml, put them against the magnet 3 wait tillsolution is clear, discard the buffer 4 respend the beads with 1 mL ofwash buffer 5 wait till solution is clear, discard the buffer 6 Repeatstep 4 & 5 for 3 times 7 Resuspend beads in 0.5 ml of Final resuspensionbuffer Store it at 4 C.

TABLE 14 Wash Buffer Composition Wash buffer [stock] [final] reagentvolume H2O 93850 1000 10 mM Tris pH 8.3 1000 1000 50 mM KCl 5000 10001.5 mM MgCl2 150 50 0 % Glyceraol 0 Total 100000

TABLE 15 Final Resuspension Buffer Composition Final resuspension buffer[stock] [final] reagent volume H2O 6770 1000 10 mM Tris pH 8.3 200 100050 mM KCl 1000 1000 1.5 mM MgCl2 30 50 30 % Glyceraol 12000 Total 20000

The sequencing results (using an Illumna sequencer) showed a 3.6-timesreduction in a number of sequencing reads mapping to 18S rRNA sequenceand are summarized in Table 16.

TABLE 16 Sequencing Results 18S rRNA no depletion 18S rRNA depletedNumber of input reads 263367 263198 Number of quality reads 262927262586 Reads mapped to 18S 96692 27142 All rRNA (%) 36.8% 10.3%

The probe sequences used were as follows:

SEQ Name ID NO: Sequence P600 38 /5Biosg/TACCTGGTTGATCCTGCCAGTAGCATATG18S_1 39 /5Biosg/CCGTGCGTACTCAGACATGCATG 18S_2 40/5Biosg/CAGTTATGGTTCCTTTGGTCGCTCGC 18S_3 41/5Biosg/GCCCGTCGGCATGTATTAGCTCTAGAATTAC 18S_4 42/5Biosg/CGTGCATTTATCAGATCAAAACCAACCCG 18S_5 43/5Biosg/GCCCGAGGTTATCTAGAGTCACCAAAGC 18S_6 44/5Biosg/CGACCCATTCGAACGTCTGCC 18S_7 45 /5Biosg/CGTGGTCACCATGGTAGGCAC18S_8 46 /5Biosg/CGGAGAGGGAGCCTGAGAAAC 18S_9 47/5Biosg/GGTCGGGAGTGGGTAATTTGCG 18S_10 48/5Biosg/CTCTTTCGAGGCCCTGTAATTGGAATGAG 18S_11 49/5Biosg/GCACCAGACTTGCCCTCCAATG 18S_12 50/5Biosg/GTTGCTGCAGTTAAAAAGCTCGTAGTTGGATC 18S_13 51/5Biosg/GGGACACTCAGCTAAGAGCATCGAG 18S_14 52/5Biosg/GAGTGTTCAAAGCAGGCCCGAG 18S_15 53/5Biosg/CCCTCTTAATCATGGCCTCAGTTCCG 18S_16 54/5Biosg/GAGGTGAAATTCTTGGACCGGCG 18S_17 55/5Biosg/CGTCTTCGAACCTCCGACTTTCGTTC 18S_18 56 /5Biosg/ATGCGGCGGCGTTATTCCC18S_19 57 /5Biosg/CCCGGAACCCAAAGACTTTGGTTTC 18S_20 58/5Biosg/GAATTGACGGAAGGGCACCACC 18S_21 59/5Biosg/GAGCTATCAATCTGTCAATCCTGTCCGTGTC 18S_22 60/5Biosg/GTTCTTAGTTGGTGGAGCGATTTGTCTGG 18S_23 61/5Biosg/GTCGCGTAACTAGTTAGCATGCCAG 18S_24 62/5Biosg/CAGCCACCCGAGATTGAGCAATAACA 18S_25 63 /5Biosg/AGTCAGTGTAGCGCGCGTG18S_26 64 /5Biosg/TCAGCGTGTGCCTACCCTACG 18S_27 65/5Biosg/GCACTTACTGGGAATTCCTCGTTCATGG 18S_28 66/5Biosg/GCTTGCGTTGATTAAGTCCCTGCC 18S_29 67/5Biosg/CGAGGGCCTCACTAAACCATCCAATC 18S_30 68/5Biosg/GCTGAGAAGACGGTCGAACTTGACTATC P601 69/5Biosg/TAATGATCCTTCCGCAGGTTCACCTACG RiboHill-1 70/5Biosg/GGGGATTGCAATTATTCCCCATGAACGAG RiboHill-2 71/5Biosg/GCTTATGACCCGCACTTACTGGGA RiboHill-3 72/5Biosg/TGCGTTGATTAAGTCCCTGCCCT RiboHill-4 73/5Biosg/TAGCGACGGGCGGTGTGTAC RiboHill-5 74/5Biosg/TGGATGGTTTAGTGAGGCCCTCG RiboHill-6 75 /5Biosg/CTTCTCAGCGCTCCGCCASEQUENCES: SEQ ID NO: 1CEPKRHQSPPPPKKRTTEEPKNRRQKIRSKYAQMQSLFKRDPKRVAAHLIKNQPLCNVSCPIDAAESALRQRLSQRPGVDAAPFTSKCPQYSKNILDPIFPEEVTLHLQKIKIHTLEGPDGIKVSHLRSCDPDCRTTLIPKTDDPHPDAEDYRPITVASCLYRLFSKVVTRRLEDSLSLHPRQKAFRSGTDGAFDNTSTLMTVIREAHNCGEELNIVSIDLAKAFDNVNHTSITRALRMHGLDDDSRTLITQMVTGSSTIIKDGGALSNRIEINQGVRQGDPISPLLFNAVMDELVERLQLTGEGFKLKGVEVTTLAFADDVTLISRSHRGIEKLLSITLDFLNERGLKLNINKCKGIRLVRTPKTKSLVEDTSKPFTVPSYGEENQHIPMVPPGDLIKFLGVDITLNGKPHFDLAPLECTLERIRKAPLKPTQKLATVRDYLIPSLEYRLGVPGISRKILESVDGAIRSAVKRFLHLPTTGMNSMFLSMPIKKGGLGLRPLTTQHMARVAVGANNMMTSMDCLSRVVADTTTLRKPLLSALEHFAVPAATKSAIREGKQNLLREEIAQLSETYHGSCLPSFKKGSLVNSWLRGTGGMRSRDYITGLKLRFGVIETRSQKWKGRTPQNPDALLCRHCGHLSGHRETAAHISQKCPTTQATIIQRHNKIVNLVGDRAKREGFAVHVEPAIKSGDAVYKPDLVLVKDDTAHILDVAAPWEKGTTMHEKHERKISKYTVLTEDVKALFDVQTCTVGAIIIGASSSWCPSNNRSLKACGLHMPKKFKRLLCRVALEGTCKIFQNFFTLT SEQ ID NO: 2CESKSHQPPPPRKKRTREEPKNRRQKIRSKYAQMQTLFKRDPKRVAAHLIRNQPLCNVSCPIDAAESALRQRLSQRPGVDAAPITSKCPQNSKNILDPIFPEEVTLHLQKMKIHTSAGPDGIKVSHLRSCDPVCLAKAFNLFLLARHIPQQLKDCRTTLIPKTDDPRPDAEDYRPITVASCLYRLFSKIVTRRLEDSLSLHPRQKAFRSGTDGAFDNTSTLMTVIREAHNCGKELNIVSIDLAKAFDTVNHTSITRALRMHGLDDESRTLITEMVTGSSTIIKGDGGALSNRIEINQGVRQGDPISPLLFNAVMDELVERLERTGEGFKLKGVEVTTLAFADDVTLISRSHRGMEKLLSITLDFLNERGLQLNINKCKGIRLVRTPKTKSLVEDTSKPFRVPSFGEENQHIPMVLPGDLIKFLGIDITLNGKPHFDLAPLEDTLERIRKAPLKPAQKLATVRDYLIPSLEYRLGVPGISRKLLESVDGAIRLTVKRFLHLPLTGMNSMFLSMPVKEGGLGLRSLSTQHIARLAVGTNSMSISTDTVSRVVADTTTLRKPLLSALEHFAVPTATKSAIREGKRNLLRAEIAQLSETYQGSCLPSFKHGSLVNTWLRGTSGMRSRDYITGLKLRFGVIETRSQKWRGRTPQNPDALLCRHCGHSSGNRETAAHVSQKCLVTHALIVQRHNKIVRLVGDRAKDEGFAVHVETAVKSGEEVYKPDLILIKADTAHIIDVAVPWEKGTNMHEKHERKTNKYAQLVDDVKALFGVQNCTVGALVIGARSSWCTSNDGSLKACGLHLPKKTDGEDLTTEADDSDAEPWQKPEHSPPHAKENTEDRNTEEQSEPYTTPQTLRTSENPEIQRRRRLHRTTTRRDCARRTDHNWTPERGTTHP QKQGPSEQ ID NO: 3 NCDGRNPPAPTNRRKRLPPPARNRSERKRCNYASFQSLFKRDPKRIAAHLIKNQPLRNVSCPIDVAESALRQRLSQRPGIDAAPFKFKRPPNSECILSPISADEVTLHLKLMSAETSAGLDGVQVSHLRQCDPMCLAKAFNCFLLARYIPPQLKDCRTTLIPKTDNPRPDADDYRPITIASCIYRLFSKIVTRRLENCISLHPRQKAFRSGTDGAFDNITTLTTIVRDAHKSGKELNIVCVDLAKAFDTVNHSSIDRALRMHGLDANSRALIAQMVTGSTTVIKGDGGVLSHKIEINQGVRQGDPISPLLFNSVMDELIERLEQSGVGYKINNTEVVTLAFADDVTLVSSSHRGMEKLLSITHDFINERGLKLNIRKCKGIRFVRTPKTKSLVQDTSKAFKVRGSGEESSCIPMAGPGEFIKILGVPIAPNGKPSFDIDTLEGTLERIRKAPLKPAQKLAIVRDYLIPSLEYKLGVPGVGRRVLDEVDASIRQTVKRFLHLPHTGMNSMFLTMPIKDGGLGLRSLRTQHLARVAVGTNSMMSSADPTSHTIASMPQHQKPLHAALQHFSVPAATKDALKKGKRQLLCAEIAELTETYQGSCLPTFRKRPVGNSWLSGLNGMRSRDFITGLKLRFGVIETRSQKWRGRTPQNPAVLLCRHCGHSTGKRETAAHISQKCPQTKNLNIQRHNKIVHLVAEHARREGFTVHVEHALKSDGQVYKPDLILTKGNAAHVLDVAVPWETGTDMHEHHERKVTKYCMISDDVKAHFGVDSCTVGAIVVGARSSWCASNKTTLKACNTHFTKRFKRLLCRVALEGTCRPLLSALEHFAVPAATKSAIREDKQNLLREEIGQLSETYRSSCLPSFKKASLVNSWLRGTSGMRSRDYIAGLKLRFGVIKTRSQKWRG SEQ ID NO: 4GAMRPEEERGPKKGRKKKKPEPSVPLNSKQRKRMAYRKVQQAYHKDPKRVVA HLFHSQPLENVSCPVESGEKALQARLGKRPPADRAPFLPKRAPLKNHLLSPISAKEVSEHLKQMNLASASGPDGVKVSHLRDIGPQCLSKIFNTFLLERHIPQVLKDCRTTLIPKVDNPRPDAEDFRPITIGSCIYRLFSKIVTSRLSQLTPLNPRQKAFRSGTDGAFDNITTVASLLKLARKTGKEINLACIDLAKAFDTVNHTSITRALHRHGVDSASIELVESMVGEATTVIINSDGTRSNVIKFNRGVRQGDPISPLLFNLVLDELIDNLDQARCGFSITKEIQVSCVAFADDITLVSGSREGMNNLLTITREFLGERGLGINHSKCKGIRFTKVPKSKSLIIDTNPNCFLIRNQQGTPEPIPMAKPGEPLKTLGINLTLEGNPTFNYPELTRILNTIKHAPLKPHQKVQIIRDHLIPLLQYKLGVPTFYRATLNNIDKSIRLTVKEILHLPTTGLHNSYLYLPLKEGGLGLKRLATQYASRVGLGLSNMATSDDAVSRAVAGLHLSLMDKAKNCLGLSEISKEAIKKAKEKLVQAEIRTLLQCHLGRSHSSFTNDTISNSWMRYPTFLSARNYIMGIKLRAGIIETRAQKWRGRSPPHPTMLLCRHCGARSRTRETDIHVSQKCLHNKKLILRRHNCVVSTLGRRATQQGFAVYYEPCIKHGETVLKPDLVIIKGDTATIIDVAVPWEQGTNLREHNSRKISKYQCLEREAAKYFNVKTVKTGSLVVGARGKWSAGNDSTLKSCGLHCSKRLKKLLCTIALEGTCAVFKH SEQ ID NO: 5LEPNRRRRGYAKATRIALNAPGKVRRRAEYAAMQRQWKTKRGLCAREALEGTWKIPARTVSLSDQEAFWRPLMESQSKNDLREPAKVGETLWGLLDPITPDEVRQILGSMSSKAPGPDGHRLSDLRSIPIDQICSHFNLWLLAGYQPKALRMGESCLIPKVKDASRPQQFRPITLGSYVGRCLHKCLASRFERDLPISIRQKAFRCMDGVAENVMILRSVLDDHKKRLAELNLVFLDVSKAFDSVSHRSILHAVKRLGVPPPLLKYVEELYADSETFLRGSGELSPSIKVRRGVKQGEPLSPHLFNAVIDWALSSLDQSFGVTVGEARVNHLAFADDIVLLSSSQPGLQRLIDQLTTHLGESGLRVNSTKSASIRIAVDGKNKRWVVDPRDSVHVGGVRIPAVAVSGSYRYLGVNISAAGMRVDAADSLASKLANLSRAPLKPQQRLYILCTHLLPSIYHQLVLSSTSKKFLKYLDRCVRVAVRRWLRLPKDTPKAYFHAKCNDGGLGVPELQRVIPLQKAGRWLKMTRSQDPVVQAAVGLEYFQKLLERWSTPELYQWGGGGITTSGHLAVAQARSLYSSVNGRGLRQSGLVSTQFDWVRSGCSLLSGRNFIGAMQLRGNLLATKLRASRGRPRVDISCDCCRTPESSGHILQVCPRTSWGARIGRHDNVAKLVARESAKRHWKVIREPAIPTPAGIRRPDLVFSKGDTAIVVDVTIVPDNAELSDAHSSKVSYYDNGAIRGWVALNTGASHITFSSVNNNWSDCMAEESKRMLKLGLGLPNSIRGTISAVVLEKGFHMYLCFKRGTFRASY SEQ ID NO: 6NHERTTKQVPENNTPARRPFKRRLHRVERYKRFQRMYDLQRKRLAEEILDGREAVTCNLKKEEIKDHYDQVYGVSNDRVSLDDCPRPPGANNTDLLKPFTPTEVMDSLQGMKNGAPGPDKITLPFLQKRLKNGIHVSLANVFNLWQFSGRIPECMKSNRSVLIPKGKSNLRDVRNWRPITISSIVLRLYTRILARRLERAVQINPRQRGFVPQAGCRDNIFLLQSAMRRAKRKGTLALGLLDLSKAFDTVGHKHLLTSLERFAVHPHFVRIVEDMYSGCSTSFRVGSQSTRPIVLMRGVKQGDPMSPILFNIALDPLLRQLEEESRGFMFREGQAPVSSLAYADDMALLAKDHASLQSMLGTVDKFCSGNGLGLNIAKSAGLLIRGANKTFTVNDCPSWLVNGETLPMIGPEQTYRYLGASICPWTGINSGPVKPTLEKWIANITESPLKPHQRVDILCKYALPRLFYQLELGTLNFKELKELDSMVKQAVKRWCHLPACTADGLLYSRHRDGGLAVVKLESLVPCLKIKTNLRLVHSTDPVISSLAESDGLVGAIEGIAQKAGLPIPTPDQRSGTYHSNWRDMERRSWERLALHGQGVELFKGSRSANHWLPRPVGMKPHHWVKCLAMRANVYPTKRGLSRGNLSKNKDSAKCRGCTSMRETLCHLSGQCPKLKSMRIRRHNKICEHLIAEASFKGWKVLQEPTLVTDNGERRRPDLIFHRDDKAVVVDVTVRYEISKDTLREAYASKVRRYGCLTEQIKDLTGATSVVFHGFPMGARGAWFPESSDVMADLNIRSKYFEEFLCRRTILYTLDLLWKSN NEQYLERLAPSEQ ID NO: 7 NEGLQGNQRLPKEKPMTARAKMRHLRLLRYRRLQELYKKDRSLAAKQVLQDMLDSKPGRNPEAVKYWAETMGKESTGIDVSVMTGRPRYRDNVWSPIYPGEVSAAVKLMDSSGATGPDGFSVRSLKCTPSRVLAKVFNLFLLEEKLPAFLMTSRTVLVPKVKEPKAPTDYRPISVSSTLVRLFHKILARRLTLASGLDSRQRGFVPVDGCAENLVVLESAIRSAKNYKRSLEVASMDIKNAFGSVAHEAIFEALSKSGAPDSFVTYVRNCYDGFASVVKLGRDTAQTTVRQGVLQGDPLSPILFNLVIDQIIRSLPETVGVQLDANTKLNSMAFADDLILLSSSEAGMRRMLGVLAGVSSKFGLIFHPGKCKYLAMIWAGKQKKMKIATDLSFEIGGGFMTPVGVTETWKYLGAYLGQIGIQPARLSLQTFLERIAKSPLKPQQKLYLIRVHLLPKLIYPLVMAPIRASMLNKLDRMVRVALTGKDGILHLPQSVPSAFFYAPIGEGGLGLMELRTSIPAMVKARFERMMNSTCHHVRAAAKGAANSNRIALANRFLRKTADGIPVTSAKLVKEYQAAKLHGSFDGKPLSEAGRVKGIHSWTCDGRMVMTGQAFCEALKIRINALPCLSRYNRGTEKPRECRAGCKTTESLNHVLQVCPRTHDMRVARHDKLVNRLGGYLSQKGFEIHTEPRIITSLGLRKPDIIAIKGEKGVVLDAQIGGAANLNAAHDAKMCYYSSSPEIKEWVTGKGAPDVSYGACIVSPQGIMSEESWKTLRGLGFSKGMLNSLVVTVMEQSTYVWHVFNRSTASYGWKRRRK RKWDSEQ ID NO: 8 MAQNPCPKPPPPAKNSRERRDREYSRVQNFYKKNRSACINSILDGNTRSQNVIPGLTKFWTETFEKNSPPDDEAPDQFVADEPRDMYKWITFYEMSQDYLDSSTAPGVDGFSAKQLRSMSPRVLNKILNLLLLSENLPNSFKMHKTVLIPKIDDPKSPGDFRPITISPVLARLLNKILAARLSKLVPISQRQKAFLPVDGCGENIFLLDYILRSSKKSSKSVAMAVLDVKKAFDSVSHHSILRALNEAKCPINFINFVRNSYDGCTTKLTCGGTSFPDSVRMNRGVKQGDPLSPVLFNLIIDSAIRKLPDSIGYVIRDGLKINCLAYADDLILVASSRAGLKTLLNIVAEHLSLRGLDLNAAKCHGLSIIASGKAKTTYVSAADSLDLDGQPIKNLGVLDTWTYLGIPFSHLGRAEKVSPDLTNLLNKLQKAPLKLQQKLYAVRNFVIPRALHGLILSKTNLKELNTLDRAIRVFLRTLLYLPKDTPLGFFHSPIKSGGLGITCFRTSVLKCRLQRIARMRSSCDGVIQAVAESDIFADEYAKLRDLIRINGNVLDTTESIKRYWAQRLHSSVDGKTLAYMDYFPQGNLWMSEDKVSQRSYVFADCVKLRINAIPTRVRVSRGRPNKEMCCRAKCFDSQRMPAFESLNHITQVCPRTHGSRIQRHDKIAKFLFKNLNNCPSRSVLYEPHFVTVDGLRKPDIIIYDDSHMVVLDVQVVSDSANLEKEFECKAKKYANDVALRSAMLIKYPFIKSFSFVAATYNNRGLIAKSSVQVLRQLGLSPRSIMVSILICLEGTLETWRIFNQSTMNAH SEQ ID NO: 9SDLEVTGRKRVARGPRAIPVLSKRKARRIEYRRMQQLWRTNMTKAAHKVLDGDAGSLPHPTLAAQLGFWKPVLEAESVDLAWPFAVGHPGVAVGDLWSPITEGEVINIRLPRTSSPGLDGLTVHRWFTEVPAILRATILNIFMATGWVPPRFRHSRTVLIPKSSDLMDPAYYRPISVSSVILRHFHKILARRVAACELLDVRQRAFIAADGCAENVAVLSAILFDARTNRRQLHVITLDVRKAFDTVSHNAIRYVLSKHGMPQIMVEYLSTLYRTAAVRLEVDGEFSDEILPGRGVRQGDPLSPLLFNLIMNEILAEVPDQVGYCMMDRNVNALAFADDLVLIGATRDGAQRSLERVMAALYRFGLELAPAKCAAFSLVPCGKTKRIKILTDPQFVAGDRPIPQLGVLHTVRYLGVRFGETGPVIQGVELLPLLERITRAPLKPQQRLKILRTYLIPRYTHNLVLGRVSYSMLRKLDKQTRAAVRRWLVLPDDVPVAFFHCPIKQGGLGIQSFETAIPRLTLLRLNRLKDSQYEMARVVGSSAWADRRMRWCRFARRRDEDWPSELHAKVDGFELREAGNVSVSTRWLDDAMVHIPSSDWLQYVKVWINALPTRIRTTRGSRRLREDVNCRGGCGVQETAAHVVQQCFRTHGGRIMRHDAVASALAGELQRGGYNVHRERVFRTREGVRKPDILAAKGTHGHVLDVQIISGARPLSDGHDRKRSYYANNADLLARISALLQVPVRNLDVSTVTLSWRGVWARESAAVLTSLGVSKAVLRGITTRVLKGSYMNFSRFNQTTATCRGRANLRMSGWGPP SEQ ID NO: 10NTAKCPKGPRFRKTATHSGTNKQQRQQRYARVQKLYKMNRKVAAKMVLEETDKIQIKLPDHDPMFKFWESEFKEGEGMPERMPKDLKESPDLKAIWDPVTEEEVRKAKVANNTAAGPDGIQPKSWNRISLKYKTLIYNLLLYYEKVPHKLKVSRTVFIPKKKDGSSDPGEFRPLTICSVVLRGFNKILVQRLVSLYKYDERQTAYLPIDGVGTNIHVLAAILNDSNTKLSELHVALLDITKAFNRLHHTSIIKSLVGKGFPYGFITFIRRMYTGLQTMMQFEGHCKMTQVNRGVYQGDPLSGPIFLLAIEKGLQALDKEVGYDIGDVRVNAGAYADDTDLVAGTRLGLQDNINRFSSTIKQVGLEVNPRKSMTLSLVPSGKEKKMKVETGKPFRANDVPLKELSINDFWRYLGISYTNEGPERLSLTIEQDLERLTKAPLKPQQRIHMLNAYVIPKYQDKLVLSKTTAKGLKRTDRQIRQYVRRWLKLPHDVPIAYLHAPVKSGGLNIPCLQYWIPLLRVNRVNKITESQRSVLAAVGKTALLTSTVYKCNQSLATLGGNPTMLAYRTYWEKELYAKVDGKDLQNARDDKASTRWNGMLHSDISGEDYLNYHKLRTNSVPTKVRTARGRPQKETSCRGGCKSTETLQHVVQQCHRTHGGRTLRHDRIVGLLQHELRRDYNVLAKQELKTGIGLRKPDLVLIKDDTAHIVDVQVARCSKLNESHVRKRSKYDKKEIEVEVKSRYRVSKVMYEACTISYKGIWDKQSVMSMRRLGVSEYCLFKIVTSTLRGTWLCWKRFNMITSVRS SEQ ID NO: 11FWKPLTPNLARVSLPSKDKVSRRRLRRADYGRVQRAWKRNRNTCLRDLLRDKRTESAPPEELXVPYWESVLRSGSSCTPGQRGRTAERTELWDPVSSKEVEQALPPLGTAPGPDSFTPKDFRAVPSAVWACIFNIFMLCGRLPDYLLESRTTLIPKRDGACNPEDFRPITVSSVVVRCFHKVIANRMSRHIQLDPRQKAFRSLDGCSEGVFLLDFILGHARRNHRPVHLASLDVAKAFDSVSHAAILDVLRSFGVPDQMVEYIASVYAGSRTRLQGDGWQSHAIHPTCGVKQGDPLSPMIFNMVIDRLFTLFPRDTGVSVGDTVLNGMGYADDLVLFATTPVGLQQLLDITAEYLSQCGLRVNAAKCFSVSLAIVPHEKKVVVATKHRFKCLGQPIPALKRSDQWKYLGVPFSPEGRLKIDPLGRLKDELEKLRRAPLKPQQRLYALRTVVVPGLYHLLVLGGTTISSLNRLDIAVRSTVRKWLSLPHDVPNAYIHADARDGGLSIPSYRWTVPRLRFHRLKALSVLCDGGGPDEMVACVGDEIKRASARLQDHGMNINTRNTYRVRFARLLHTSNDGAPLKGSKKVEGQHRWVTDGSLMLSGRDYIACNWVRINSIPLRKRTARGRVRDTRCRAGCDSTETLHHVLQQCHRTHDMRIKRHNACVKYLLDRQRSRGKTVFWEPHFHTAGGLLKPDSVILHDASTAVVVDALVAGERSDLDREHDRKVSKYEPLVDLVKDRYSVDKVIFSSLIISARGVWGGRSFRHLSKLRLLDISDAKVLSTRVLLGGMGAVRVFNRRTAVSGRVNGW SEQ ID NO 12:EVFPAPPPRRERRRKKTPNPAPMRKREARRCEYGAAQSLWKRDRRHCITNILNEMGPVNQPPRETMEPYWTRMMTTDGRTSPPSDKVPIKEDIWTPITGNDIKRSRIPRASAPGPDGISARLYRSIPTTVIIRLFNLLLWCERLPEDLLLSRTIFLPKKTNASEPGDFRPITIPPVLVRGLHKILAKRLETALDIDPRQRAFRSMDGCADNTLLLDTLLRYHRKQYKSLYMASIDVSKAFDAVTHPTIESTLISLGVPPPMIRYLGQVYANSRTRIEGDGWTSKPVHPKRGVRQGDPLSPILFNAVTHRLLQRLPREVGARLGNIPINAAAYADDLLLFASTSMGLQQMIDTMTDYLAECGMTINVEKSMTVAIRAAPHLKKTAVDASLSFSCGGRQLPSLKRTNKWRYLGVVFTPEGRAQCRPAEVVAPLLGALTKAPLKPQQRLYALRTVVIPKLYHQLALGAVTIGTLNKTDRLVRGALRKWLALPHDTPNAYFHTSVRDGGLGIPAIRWTAPVQRRGRLLGVMKALGQQGLDRFIQDELNTCKKRLTDHGVLLGTPEMVAKRWAQQLYGSIDGAGLKDSAKTPHQHQWIADGSKFLTGKDFINCNRARIGALPTRSRTTRGRPQDRRCRGGCLAQETLNHVLQHCHRTHGQRIKRHDAVVKYIARNMPRSGYEVHQEPHYKTELGLRKPDLVAVLGQTAIIIDAQVVSEQTNLDDAHTRKVAYYNEPATIRAIKAEHGVRTVKVTSATLSWKGVWSPRSAEELRKLGFIRAGDAKVVATRVLIGNIAAFRTFNATTSVEHRAGIG SEQ ID NO: 13SKEPAAHPPLPFGARRPPDKKRARRRWEYAAVQRAFRKNAARCVNGLLDGTLL HQPPSIPGLVEFWKDLFTAPCASSRPRSKEGLSPMLLASSQPVSFRDLWAPITSEEAAAALPPRNSAAGPDALTPAQLRRLPHPVFLKILNLFLLARSLPSRLLRARTTLLPKKTSPASPADFRPITVCSVLARAFHKVLAGRLMRYCVLDGRQRAFIPQDGMLHNSFLLDLAMAHSRRTACSLYVASLDVSKAFDSLDHGALSPVLRAHGLPVEFVEYVRGCYQASTTVICGGGSSSDLVRPSKGVRQGDPLSPILFNLSIDLLLSRLPGYIGARIFSRRVNAAAFADDILLFAETKGGLQELLSTATSALGDLGLEVNPFKCFSLALVASGREKKVKVDNSVIFRAGNKNIPALAMGDTFRYLGLQFSTSGLSQFHPRQEVQEQLDIIKRAPLKPQQRLFALRSVILPGTYHGLALGRTRLGALKSLDVCVRAAVRAWLRLPDDTPIGYFHAPVIYGGLGIPATRWLGPLLRRRRLASMEGLGVIVDEPSQDILKREICRLDNYLKWDGDVIKTSYQLGRFWALRLHSSVDGAALRRSAQTPGQHSWVSNTRLMLSGRDFLACVRARISALPSRARLLRGREGDTRCRAGCNASETNNHVIQHCWRSHEARVERHDAVALYMVRGLRRRGYDVHRELHLRTSQGLKKPDIVAVSGTTAFVIDAQVIGDHLDADRCHREKVEVYDQQPVHTEIKRMFPEVQMITTTSATLNWRGVWSPASAKALIGIGENSNHLSTMATRALLGSIMAARRFDSMTAPRRRMMPRTGVG SEQ ID NO: 14NRNDRPSSATVPARRPRNRRISRRQQYARCIKSLLDGTDESALPNQSIMEPYWRQVMTQPSPSLCSNTVPRKGNMQEGVWSPITSRDLQVHKVPLTSSPGPDGITSQTARSIPIGIMLRIVNLILWCGDLPVPFRMARTIFIPKTVRANRPQDFRPISVPSIVVRQLNAILASRLTAAVSWDPRQRGFLPTDGCADNATIVDLVLRDHHKRYASCYIATLDVSKAFDSVAHDAVFNTVTAYGAPKSFVDYVRRWYSGGGTYFNGGDWRSEEFVPARGVKQGDPLSPVLFNLIIDRLLRSLPKDIGVHVGNAKVNACAFADDLMLFASTPKGLQELLNTTVKFLSSVGLTLNADKCFTISIKGQPKQKVTVVEQRTFCIGRARVQLKRSEEWKYLGIHFTADGRARYNPSEDIGPKLERLMQSPLKPQQKLFALRTVLVPQLYHKLTLGSVALGVLRKCDKLVRSFARKLLGLPLDVSVAFYHAPHSCGGLGIPSVRWIAPMLRTKRLAGINWPHLEQSEVASAFLSEELRRARDRAKAGVNELLSQPKIDTYWADRLYTSVDGNGLREARRYAPQHGWVSQPTRLMSGKAYRTGIQLRINALPTRSRTTRGRHEMNRQCRAGCDAPSHNHVLQRCHRTHGSRVSRHNGVVSYLKKGLETRGYTVYSEQSLHGQNRVYKPDIVAFRHDSTIVVDAQVVTDGLDLDRAHQSKVEIYNRQDLLTTLRSVYRARENIEVVSATLNWRGIWSFQSITRLRTLGILTAGDSNVISSRVVSGRVYSFKTFMFHAGFHRGMA SEQ ID NO: 15SSGRKLPVKSRGARETVQKKMANPRVAKYKRFQRLFRSNRRKLASHIFDKASLEQFGGSIDEASDHLEKFLSRPRLESDSYSVINGNKSIGVAHPILAEEVELELKASRPTAVGPDGIALEDIKKLNSYDLASLFNLWLKAGDLPESVKASRTIFLPKSDGTTDISNCRPITIASALYRLFSKIITRRLAARLELNVRQKAFRPEMNGVFENSAILYALIKDAKARSKEICITTLDLAKAFDTVPHSRIVRALRKNNVDPESVDLISKMLTGTTYAEIKGLQGKPITIRNGVRQGDPLSPLLFSLFIDEIIGRLQACGPAYDFHGEKICILAFADDLTLVADNAAGMKILLKAACDFLEESGMSLNAEKCRTLCISRSPRSRKTFVNPAAKFNISDWKTGISSEIPSLCATDTFRFLGHTFDGEGKIHIDMEEIRSMLKSVRSAPLKPEQKVALIRSHLLPRLQFLESTAEADSRKAWLIDSIIRGCVKEILHSVKAGMCTEIFYIPSRDGGLGLTSLGEFSLFSRQKALAKMAGSSDPLSKRVAEFFMERWNIARDPKVTEAARRVYQKKRYQRFFQTYQSGGWNEFSGNTIGNAWLTNGRARGRNYVMAVKFRSNTAATRAENLRGRPGMKECRFCKSATETLAHICQKCPANHGLVIQRHNAVVSFLGEVARKEGYQVMIEPKVSTPVGALKPDLLLIKADTAFIVDVGIAWEGGRPLKLVNKMKCDKYKIAIPAILETFHVGHAETYGVILGSRGCWLKSNDKALASIGLNITRKMKEHLSWLTFENTIRIYNSFMKN SEQ ID NO: 16TKWRPSKPRLPPTYRANTSRKHLRRLQYGHIQTLYNRCRRDAANTVLDGRWRSPHTSSPFSIPEFETFWKTIFTTPSTPDNRPVVPVLPTCPALLDPITPDEITWALKDMRNSAPGVDRLSAQHFLNFDVPSLAGYLNMVLAFKFLPTNLSISRVTFIPKGASPQQPNDFRPISIAPVITRCLHKILAKRWMPLFPSSKLQFAFLQRDGCFEAINLLHSLLRHAHERHSGCSIALLDISRAFDSVSHHSILRAAHRFGAPDGLCQYLQRVYNGSTSLFNTVDCAPSRGVKQGDPLSPLLFIMSLDEALESIETVSPVIVDGLPISYIAYADDLVILAPNADLLQKKLDKLASLLQRSGLIINTSKSMSIDLIAGGHSKLTALKPTVFKIDGNQLQRLNVSDHFDFLGISFDYKGRSKMDHVETLSAYLLNLTQAPLKPQQRMSILRENLEPRLLYPLTIGVVHKCTLRQMDCLIRSSVRKWLRLPSDTPTSFFHSSISTGGLGIPHLSSIIPLHRRKRAAKLLLSPCPIIRWVSQSPSFSNFLRICNLPINVHRDLIHSFDEARCSWSKQLHSTCDGRGLSMSSRNTVSHLWLRYPEHIFPRLYINAIKLRGGLLSTKVRRSRGRQENADLLCRGRCGHHESIQHILQHCSLTHDIRCRRHNDICRLVASRLRRNNIRFFQEPCIPTPVSFCKPDFIIIRDSIAYVLDVSVCDDANVHLSRQLKINKYGCSTVVSSIYNFLNATGLRISSVRQTPLIITYRGLIDPLSTTSLRRLSFSSRDISDLCVASIQGSMRIYNTYMRGTSPQDP SEQ ID NO: 17QHALDCFPRLWAPSRPRPNHPQPRSYRALRKAQYASLQRILHTSPKDAATHVLDGSWRLLHQNRALPPDLHSFWTNVFRIPSFSDNRPVSATQPELSLISPITCEEVKKAIAGMGGTAPGLDRLTPANLKSFGLKPLTGYLNLILCYGCPASLAAARVTLIPKVPDATRPEQYRPLAVSSVIVRCLHKILAFRWASVLKLSSLQLAFMQRDGCLEATTILQGVFRDAHSRRRPIAMAFLDVSKAFDTVLHDSVFRAAAMYGAPPLLLRYLRKLYSQGTVTLGDIDILPKRGVRQGDPLSPLLFILAMEEILMAANPNDGYQLPSSTISTLAYADDLVLFAHSPGALGLKLERVAAALRLAGMEINAAKSITFTISANTHNKNLCLENIAYTLDGVSIAAADTETRVKYLGLHFNWKGQISYKDTARLAGYCQELTSAPLKPQQRIHILRQVALPKLHHQLVLSSIHRRTLKAMDISCRHYVRRWLKLPQDTSTAFFHAKIGDGGLGLTSLATSIPLWRRTRLTKLITSEHPVVRDVVSICLTKALAVANEPVFVMGTVVSDKDEAAMAWKLAMYATLDCADLQTIHETPESSNWVVRPLRMTPSLYIRGLQLRAGTLGTKSRQQRGRAQMDKLCRRGCGQTETLPHILQSCPAAHAARCVRHNRVAKSIAVSLRRKGYRVYEEPIIRTGTTYCKPDIIACQDGLGFVIDVAVVSGHRLHESWDLKIAKYDTDFINTAIIDCLPEDVEILSLIHQPAIISFKGVWFPPSAKRLKTLGLSADCLAGLGLVTIKGSLACFDMFMMGSNG SEQ ID NO: 18KENLKKRACKTLTRRIKPKKSKKHEYWKMQQMYHRDRAGLAKLILEGEARDICPIPLTRLTTAFKEKWEKEDRFVSLGQFKSSCKAVNDIFASPISPEEVCKIRSKMKNKAATGLDGISKTCLMRGDPKGINLANLFTAILLNGYIPRALKKNRTTLLPKTQDKRKLSDTSQWRPITIGSTIQRLLSGVINDRLKEACEIHPRQRGFISSPGCAENLMLLRELIALSKRELKPLAVIFIDFAKAFDTVSHKHIKAVLQQRGVDKMIIDLISNSYEGRTTILKAKGSYSREIRLKMGVKQGDPLSPLLFNLAIDPLLCKLDKVGEGAIVDGIEITSLAFADDIVLLSNSWSGMRKNLKILEVFCELTGLTLNVMKCHGFFIDSMNRCLAINECPPWRLQQNDLHMIGSKEKEKYLGMEISPWLGIIEPNIQKMINIMLNNLTASLLKPSQKLELLRTYAVPKLTYMADNGMVTQTTLITTDRKIRMTIKKWFHLNHATTDGLLYTGCKSGGMGLVKLARVIPRIQVNRILGLCNSEDSCTRTMARKAHRPSEFRKIWKMGMGKGGETTIQGASDIRTPYWNTPKIHSDWRINELDKWKKMKTQGEGIEVFENDKISNSWLRHPTLSNFSERDYILALKLRTNTYPMKAILARGRMAKNKGTKCRLCGYIKKTTKHVLGSCIGTRPNRMQRHNKICALLAKAARQLGWETLTEHHLKMDNGKTLVPDLIMMKDTRAIVADVTICYETNQYSLRKAYEVKVKKYAPLELPIKERWPGIKDVRIHGFPLGTRGKWPSLNWRLLEELDMDKSKRRKFASLLSKRSLLYTIDILK WFSKNSEQ ID NO: 19 TRSAPSSTSSGKSTRNAKRLEKLKKYGYYQHLYYNNKKKLVAEILDGETSGAKPPPMNLVEDYYKNIWSRSTIDDSPVNNIKTVNSDSIFAPISRDEIKLALSNTKKDSAAGPDSVTIKEAKAIIDNLYVAYNIWLGVQGIPEQLKLNKTILIPKGNSDLSLLKNWRPITISSIILRVYNRLLAYRMNKVFKTNDKQVGFKPVNGCGINISWLHSLLKHARLNKNPIYACLVDVSKAFDSVSHQSIVRALTMNGAPSLLVKLIMDQYTNINTIITCSGSISNKINISSGVKQGDPLSSLLFNMVIDELFDVIKDQYGYTIDNIGTTNARCFADDLTLISSSRMGMNKLLELTTEFFKERGLNVNPSKCMSIGMSKGYKGKKSKIESEPLFSIADAQIPMLGYIDKTTRYLGVNFTSIGAIDAKRIKKDLHDTLDKLEHLKLKAQCKMDLLRTYMIPRFMFQLIHTELYPKLLIKMDILIRKLAKRILHLPISTSSEFFYLPFKEGGLQLTSLKEAVGLAKIKLHKKIMSSNDPMLCYLIESQRSRIIEHFMKDLKLGDSLTLNEMDNIKECFMKEKRISFAQKIHGVGFEVFSSSPLTNQWINGEIKTMTTRTYINSIKLRTNTLETRVTTSRGLNIIKTCRRCHVADESLMHVLQYCSSTKGLRYSRHHRICAKVANKLMKNGYGVYREKSYPDPNNSGSYLRPDLIAVKDGHVIVLDVTVVYEVTGATFINAYQTKVNKYNTIMVQIEQMFNCVSGVLHGLVIGSRGSIHHSQLHIWHQMGFSSTELKYVAIGCMEDSLRIMSTFSKAIL SEQ ID NO: 20KSKSLPRLKRTGRAFHRREKYAICQKSLDKDFSGTISKILDGVEISEAEVRPEMAKIEEVYQQRLGNTSGALPENTDTPVVEGLRFERKTAPFDAQEVTRAIRESNKSTAAGPDRWFNGRCLKNLDCETVAALFNLWRFKQKIPSALRENRTILLPKGGDLTDANNWRPLTIGSLLLRLYAKSLTTRWSDAPICERQKAFRPVDGCWENINLLLGALKSAHKKRRQINLISIDLAKAFDNIQHGAIFNAMRRFGFSPSEISVVKDLYTNVWTKISIGNEISGPINISRGVKQGCPLSPFLFNLVLDELINELQSSGYGYPVEGFKVPVLAYADDLILCGATDYETKRMVEITEKFFARQMLAVNLKKCKALRLLPVKGKRTLKVSSDPMLWKGEQLPMVKSIDDFISYLGVKVSVTGKVIWSVDQLRLWLDRVMKAPLKPDQKIKGIKEVLIGRLTYQLRLSEARVCELRRVTRMVRKACKQILHMQLGAPNAWAHLPLRKCGLGLPDFELTIPLMRRAACEKMKSSPDPVVANISEKIPIYESGLTRGLDVRAAKRAIQDKYEQAYLSTQRGKLMNARWISAVKPYWLHGGTGVVKAGEYVSINKLVTRTIETRQFIHPGVTDFETLKCRRCGKAVETDLHVLNECPFTRLAQCRRHNFIADYLGKVLVDHGWEVWRERLVKKDLENFKPDLICRKGAEGAIIDVTVPYESNEAVLQSKERFKEAKYAGLKGQVAELLNINGGVKVVGIAVGALGTILTSTLEKAKGLGLDPVKVGKSLQISALRGSG HVWKAFRS

What is claimed is:
 1. A method for simultaneously amplifying aribonucleic acid (RNA), the method comprising: (a) providing a reactionmixture comprising said RNA and a non-naturally occurring enzymecomprising (i) a finger domain derived from a non-retroviral transposonor from an R2 retrotransposon; (ii) a thumb domain derived from an R2retrotransposon; (iii) a palm domain derived from an R2 retrotransposon;and (iv) an endonuclease domain derived from an R2 retrotransposon; and(b) subjecting said reaction mixture to conditions sufficient tosynthesize a complementary deoxyribonucleic acid (cDNA) library fromsaid RNA.
 2. The method of claim 1, wherein said non-naturally occurringenzyme further comprises a fusion-tag molecule.
 3. The method of claim2, wherein said fusion tag-molecule stabilizes said non-naturallyoccurring enzyme.
 4. The method of claim 2, wherein said fusion-tagmolecule is selected from the group consisting of: Fh8, MBP, NusA, Trx,SUMO, GST, SET, GB1, ZZ, HaloTag, SNUT, Skp, T7PK, EspA, Mocr, Ecotin,CaBP, ArsC, IF2-domain I, an IF2-domain I derived tag, RpoA, SlyD, Tsf,RpoS, PotD, Crr, msyB, yjgD, rpoD, and His6.
 5. The method of claim 2,wherein said fusion-tag molecule is selected from the group consistingof: His-tag, His6-tag, Calmodulin-tag, CBP, CYD (covalent yetdissociable NorpD peptide), Strep II, FLAG-tag, HA-tag, Myc-tag, S-tag,SBP-tag, Softag-1, Softag-3, V5-tag, Xpress-tag, Isopeptag, SpyTag, B,HPC (heavy chain of protein C) peptide tags, GST, MBP, biotin, biotincarboxyl carrier protein, glutathione-S-transferase-tag, greenfluorescent protein-tag, maltose binding protein-tag, Nus-tag,Strep-tag, and thioredoxin-tag.
 6. The method of claim 1, wherein atleast one of said finger domain from an R2 retrotransposon, said thumbdomain of an R2 retrotransposon, or said endonuclease domain of an R2retrotransposon is derived from an arthropod.
 7. The method of claim 1,wherein at least one of said finger domain from an R2 retrotransposon,said thumb domain of an R2 retrotransposon, or said endonuclease domainof an R2 retrotransposon is derived from silkmoth.
 8. The method ofclaim 1, wherein at least one of said finger domain from an R2retrotransposon, said thumb domain of an R2 retrotransposon, or saidendonuclease domain of an R2 retrotransposon is derived from avertebrate or an echinoderm.
 9. The method of claim 1, wherein at leastone of said finger domain from an R2 retrotransposon, said thumb domainof an R2 retrotransposon, or said endonuclease domain of an R2retrotransposon is derived from a flatworm or a hydra.
 10. The method ofclaim 1, wherein said non-naturally occurring enzyme has at least 80%identity to SEQ ID NOs: 1-20.
 11. The method of claim 1, wherein saidhost is selected from bacteria, yeast, algae, cyanobacteria, fungi, aplant cell, or any combination thereof.
 12. The method of claim 1,wherein said host is E. coli.
 13. The method of claim 1, wherein saidnon-naturally occurring enzyme comprises a mutagenized motif-1 sequence.14. The method of claim 13, wherein said mutagenized motif-1 sequencehas an improved jumping activity as compared to a wild-type sequence.15. The method of claim 1, wherein said non-naturally occurring enzymecomprises a mutagenized motif 0 sequence.
 16. The method of claim 15,wherein said mutagenized motif 0 sequence has an improved jumpingactivity as compared to a wild-type sequence.
 17. The method of claim 1,wherein said non-naturally occurring enzyme comprises a mutagenizedthumb sequence.
 18. The method of claim 17, wherein said mutagenizedthumb sequence has an improved single-stranded priming efficiency. 19.The method of claim 17, wherein said mutagenized thumb sequence has animproved processivity.